A Time to Heal
by PyroDragon2006
Summary: John thought it was over, but when a new presidential advisor and an old enemy both show up on Atlantis, the wounds run deep. Set after Common Ground, so SPOILERS! Now COMPLETE!
1. Teaser: A Time to Die

Disclaimer: Stargate: Atlantis and all characters therein are the property of MGM. This story is for entertainment only and the author is in no way profiting from it, nor exercising any claims to Stargate Atlantis.

Title: A Time to Heal

Author: Pyrodragon2006

A/N: This is a new story I've been toying with for a while but didn't have time to write. Its independent, but does _take place directly after the episode Common Ground, so major spoilers!_ I'm still working on Fate's Fickle Humor, but my muse has a fickle humor, too, so its slow going. This one is for my beta, my sister, Cindy, who turned 19 today. Happy Birthday!!!

Teaser Chapter... A Time to Die

A short time into the future...

John came awake to a nightmare, trapped in darkness, some sort of rough cloth covering his eyes, but the position of the rest of his body was all too familiar. His hands were bound down to his sides as he sat in a chair, the rough metal of the shackles biting into his wrists as he instinctively began to struggle. Shackles also rubbed at his ankles, keeping his legs secure, and sending his half-lucid mind spiraling down into the depths of uncontrollable panic.

_No! Not again, never, would die first! Must get out, get away, run-!!_

He jerked his body around wildly, to be free the only thought, heedless of the pain or the slick blood that began pouring from newly torn flesh, or the agony stabbing through his head.

_Hands! Hands touching, pulling-! No!_

He would not be Kolya's toy, an amusing diversion until he finally found the release of death, then thrown away, discarded where no one would ever know his fate. _Fight!_ He had to fight until he got free, found a way- or forced them to kill him. He seized on that thought, using it to boost flagging energy. Mustn't let them near, let them take the blindfold off to force him to watch death come once again. This time he might break... He would stay, hide, in the darkness. A voice tried to intrude, to trick him into stilling, coming out, but he would not allow himself to weaken and hear what it was saying. What _he_ was saying.

His body betrayed him eventually, desperate flailing around slowing, then stopping, as strength ebbed. Hands were on him again, sending alarm, along with overwhelming fear, coursing through his veins, but he could no longer even keep his head up. Cloth was pulled away, allowing bright light in as well as agony spiking through his head. His vision blurred, colors and objects running together, making no sense, so he squeezed his tortured eyes shut despite the pain the move caused. A light touch near his right eye and subsequent shaft of shooting agony, galvanized him to resume the frantic, and useless, squirming as he jerked his head away. John attempted to curse, yell, insult whoever had him, but this time he'd been robbed of his voice as well. An attempt to swallow added his throat to his growing list of pain as it throbbed and burned mercilessly, reminiscent of the morning after screaming his throat literally raw at the homecoming game. This time, it wasn't so pleasant. Even his slimmest illusion of control- his ability to insult and make light of things- gone. Pressure on either side of his face stilled his head, and he sensed a presence just in front of him. The energy he had momentarily found had fled once again, leaving him too weak to break from the grip.

"Look at me!"

The stern command in that cold, demanding tone sent cold shock to his core, bringing with it the welcome veil of unconsciousness, but also dreams of safety, of Atlantis...


	2. Ch 1: A Time to Live

Disclaimer: Stargate: Atlantis and all characters therein are the property of MGM. This story is for entertainment only and the author is in no way profiting from it, nor exercising any claims to Stargate Atlantis.

Title: A Time to Heal

Author: Pyrodragon2006

Chapter 1: A Time to Live

Not that long before...

Lieutenant Colonel John Sheppard, military commander of Atlantis, was not a happy man at the moment. It was taking way too much energy to force his tired, sore body through the halls toward his office at anything remotely approaching his normal, brisk pace and he was already late. With an exhausted half-pant, half-sigh, he gave in, slowing a bit while mentally chewing himself out, knowing Elizabeth wouldn't be too pleased with him. Not that it mattered, since this week already topped his 'I wish I'd never heard of the Pegasus Galaxy' list and showed not signs of having mercy on him any time soon.

The whole thing had certainly started simple enough, with a request from supposed friendlies for John's team to help them explore some ruins. Which waltzed them right into an ambush by renegade Genii and ended with John himself enjoying the hospitality of Acostus Kolya. Complete with torture by life-sucking alien for revenge and an internal Genii squabble, telecast in living color for his team and half of Atlantis. He was thinking of recommending it as a 'gem' for the Triple-A tourist guide to the Pegasus Galaxy. He'd managed to escape, but only after more than forty years of his life had been ripped from him, and only by teaming up with, believe it or not, an _honorable_ Wraith. One who'd even had a sense of humor scarily close to his own. After getting themselves thoroughly lost, the Wraith had fed a _fourth_ time, killed a bunch of Genii, and, just when John was certain he was a dead man, gave the colonel back the life he'd taken. Naturally, John's team had chosen that moment to show up, pulling the alien off him before the thing could heal the minor stuff, mostly dehydration and bruises from the guards using him as a punching bag when he didn't cooperate. That was most of the time.

Next came three fun filled days in the infirmary being poked, prodded, tested, and monitored while suffering from the inevitable nightmares. Thankfully, Carson Beckett had acted like a Scottish bull dog, carefully guarding his friend and patient against overzealous scientists and unintentionally intrusive friends. John knew it would take time to recover from this, especially mentally, but he really was getting better. The nightmares no longer thrust him awake screaming, just gasping, and usually after two to three hours of actual sleep, not one.

Still, it was wearing him down so when he'd been released to his quarters to convalesce yesterday morning, only to find Rodney McKay camped out waiting for him, it had taken all his control just to stay civil. The man had been harboring a lot of guilt, misplaced if he had bothered to ask John, that he hadn't somehow come up with some miraculous way to find the planet Kolya hid on and get to him sooner. The socially awkward scientist couldn't come out and _say_ that, so he hid behind complaints and somewhat tactless questions about the feedings, but John had grown adept at reading between the lines with his friend. He'd tried to answer, to reassure Rodney that he really was all right, but it grew more and more difficult to control the flashbacks and associated emotions, finally driving John to lock McKay out of his room. All he truly wanted was a return to the normal, the routine, but everyone treated him like cracked glass, ready to shatter at the least pressure. Going through the mandatory debrief with Elizabeth, Carson, and Dr. Kate Heightmeyer, the base psychologist, had been about all he could take, so after kicking Rodney out, he'd simply refused to answer the door or leave his room.

Which, eventually, landed him in deep, hot water with a certain Scot when the physician came to check on him, make sure he'd eaten. He hadn't, since it meant going to the mess hall and dealing with all the well-meaning but dreaded questions of the scientists on the scent of a scientific mystery. Some of them, like Dr. Malenkov for instance, were worse then a pack of blood hounds. Then there were the stares of everyone else, full of pity, sadness, guilt, sympathy, or even contempt. That last one was the hardest to deal with. He'd made a deal, even a tentative friendship, with one of the mortal enemies of Atlantis, who'd then called him 'brother', or at least that was the current version making its way through the Atlantis grapevine. How did he explain the necessity, the corner he'd been in, to those who'd lost friends and loved ones to those same alien monsters? Some had obviously decided not to even try understanding, and nothing he said would be changing that. John's biggest fear upon returning had been that his Satedan friend would react that way, but Ronon had bluntly disabused him of that during his endless, dark first night back.

Carson had brought him meals yesterday, which he'd dutifully picked at, but insisted John face his apprehensions today lest he wind up unconsciously confining himself to his quarters through fear. Except the doc's plan backfired. John had slept poorly last night, even between bouts of nightmares, falling into a semiconscious state of exhaustion he'd finally woken up from late in the afternoon. True to his word to Carson, he'd made his way to the mess hall-

Just in time to walk right into the middle of a fight between four of his marines. He'd tried breaking it up only to have one man swing before checking to make certain of the identity of his target. The low jab had landed on his left side, right on top of a nasty bruise courtesy of the Genii, doubling the colonel over for an instant before half falling into a mess chair. The only upside was it had stopped the fight cold, visions of court martial no doubt dancing in their heads. And just what had started the whole thing in the first place? A less than respectful remark about John himself uttered by one of a duo brought in on the last _Daedalus_ run, making the mess more than a little awkward for their tired, hurting CO to deal with. Fortunately, Major Leonard had tactfully insisted on taking over, citing the fact that the colonel wasn't even supposed to be on light duty at the moment.

He'd then glanced down at his watch only to realize he was late for the meeting Elizabeth had finally called about some VIP passenger supposedly coming in on the next run. The likely fireworks from Rodney would have been entertaining to say the least, but by now the Atlantis leader was no doubt ready with some fireworks of her own for John since he'd begged, cajoled, and pleaded with her and Beckett to be allowed to attend. He'd even put on his uniform, trying to _look_ normal even if no one was letting him feel that way. 'Course, he'd forgotten not only his com, but the relevant files Elizabeth had given him last week on his desk in his office. Get the things, get his sorry butt to the conference room, and hope he could brush off their worry, that was his current plan.

He needed this, the distraction normalcy provided. Why didn't they understand that sitting around with nothing to do but go over and over that hell in his mind would truly drive him insane? He just wanted to be a part of life again, to forget... As much as Kate let him, anyway. _That _was a neon colored shoe he kept waiting to have dropped on his head despite the assurances of both her and Carson that they would be allowing _him _to tell _them_ what he needed to recover from this, not the other way around. The problem was that he wasn't sure how to go about doing that besides going on, and everybody else seemed to believe that was the wrong answer.

Finally, his office, files stacked neatly on his desk illuminated by the light of the afternoon sun streaming in the windows... And a chillingly familiar shape sitting there.

"No, no, no, no-!"

His nine millimeter was out of its holster before he could consciously command his body to move, finger frantically pulling the trigger over and over. The successive barks of the weapon echoed in the small room, setting his ears to ringing even as the bullets kicked up sheets of paper and a myriad of other small items from his desk, obscuring his target.

_Still there, a threat, kill it. Still there..._

The litany ran through his mind as his heart threatened to beat right out of his chest, eyes darting around the room.

_Shoot! Must keep shooting!!_

_Click, click, click..._

Lost in a haze of fear, anger, and alarm, the exhausted colonel never realized he'd emptied his clip with his enemy still sitting there, apparently untouched...


	3. Ch 2: A Time for Anger

Disclaimer: Stargate: Atlantis and all characters therein are the property of MGM. This story is for entertainment only and the author is in no way profiting from it, nor exercising any claims to Stargate Atlantis.

Title: A Time to Heal

Author: Pyrodragon2006

Chapter 2: A Time for Anger

_Tap, tap, tap. Tap, tap, tap._

Dr. Elizabeth Weir, leader of Atlantis, drummed her fingers on the briefing room table, staccato beat emphasizing her worried thoughts. Not to mention providing the beat to her steady mental cursing in at least ten languages. She should never have allowed her military commander, Lieutenant Colonel John Sheppard, to talk her into letting him come to this meeting. The one he was, let's see... twenty- _two _minutes late for? She should have listened to her gut, not let him talk her into it, that's what it came back to. The problem was he'd asked, and she hadn't been able to deny him, not now. Not after Koyla- The Atlantis leader jerked her thoughts away from _that_, distracting herself by assessing the others waiting with her and their reactions.

Directly to her right sat her chief medical officer, Dr. Carson Beckett, whom she caught glancing anxiously from the clock to the empty doorway. He was as worried about their absent colonel as she was, maybe more so. Like her, he'd quickly given in to the man when he'd plead his case for attending even though he wasn't supposed to be on duty. Dark circles under the Scot's eyes spoke of too many sleepless nights lately, mostly keeping the colonel company as the nightmares took hold, his own dreams filled with what had almost been. As the expedition physician, Carson had known only too well that they really had no hope of rescuing their friend in the end, just recovering him so he could die with those who'd become his family. He'd begun making comments about the possibility of leaving Atlantis recently, and she had to wonder if the events of five days ago would be the final push he needed.

Next to the doctor was a conspicuously empty chair, then the head of the science department, Dr. Rodney McKay. He was absorbed in something on his laptop, muttering to himself while completely ignoring the rest of the room. He showed all the same signs of lack of sleep that Carson had, making the Canadian's moods even more mercurial than normal this last week, so it was probably a blessing in disguise that John's absence would make this meeting run long. It gave the science staff a breather before someone threatened to throw their chief off another balcony without the personal shield!

Then there was Teyla Emmagen, leader of the Athosian people, and a member of John's team, as was Rodney, of course. Native to the Pegasus Galaxy, the petite woman had nonetheless become an integral part of Atlantis, often acting as Elizabeth's deputy. Of them all, Teyla was also showing the least effects from recent events. Always serene, extruding a controlled competence, the only give away was the deep sadness in her dark brown eyes.

Just behind her, leaning casually against the wall as was his habit, was the last member of Elizabeth's core staff, Specialist Ronon Dex. Better known as a Satedan warrior and one man destruction team to anyone or anything that threatened his friends, especially John. His inability to dish out any damage to the renegade Genii had left him irritable, a scowl his constant expression, to the point where even the marines were ducking him for practice sessions, mostly out of self preservation. She shuddered to imagine having the large man as an enemy, almost pitying the next opponent the team came up against, provided it wasn't a certain Genii, of course. At the moment, worry, anger, and frustration emanated from him so thickly she could almost see it.

Collectively, they were an incredible bunch, but the failure to save one of their own from the worst torture any of them could think of still stung. Not exactly the best timing for the announcement she had to make, but she'd been putting it off too long already. It was time, John or no John. Carefully, she cleared her throat, four pairs of eyes instantly focusing on her with varying degrees of startlement.

"We need to start. Hopefully, when Colonel Sheppard arrives, he can catch up. First off, I need to apologize for not telling you about this sooner, but given recent events, I trust you'll understand. As all of you are aware, the SGC was considering pushing back our check-ins to once a month due to the expanded Ori threat in the Milky Way. Last week that became official when they were forced to cut short the transmission and have us close the gate."

"Well, _why_ are we cutting back? What's the SGC so afraid of? And where's the _Daedalus_? Aren't they overdue?"

Elizabeth ducked her head to hide a smile at Rodney's barrage of questions. Somehow, the man made the ship being three days late into a personal insult against him.

"They're worried about the possibility of the Ori tracing a wormhole back to Atlantis. Remember, these people were Alterrans at one point, so Earth would rather exercise caution where the continuing existence of Atlantis is concerned, Rodney. As for the _Daedalus, _we don't know, and if they've been forced to radio silence due to the Wraith, we may not until they get here. However, General Landry was starting to mention something about the _Daedalus_ when he had to cut off." She paused, steeling herself for the explosion she was sure was about to come. "What you _haven't _been told is that they have a VIP passenger aboard who will be spending the next several weeks with us, learning about our operations here. He is supposedly a new presidential adviser on the Stargate-"

"Oh, come _on_, Elizabeth!" Right on cue, the chief scientist burst in, hand slamming on the table within millimeters of his precious laptop. "What does Earth think we are, a tourist stop?! We just got that 'Wooly' guy out of our hair and now _this_! I have enough time wasted with the brain dead morons working for me without-"

"Rodney! That's enough!"

His anger was expected, but as his volume climbed, she found herself coming closer and closer to completely losing her temper with the man. Did he really believe she was any happier with this whole mess? First the IOC, now the president's man looking over her shoulder, not exactly the stress reducing measures Carson and Kate had been bugging her to take! Slowly, she counted to ten mentally, than made eye contact with each of them.

"We _will_ be polite to the man, allow him to ask his questions, and not insult him or threaten him with physical violence! I-"

_Beep, beep._

Apparently she wasn't allowed to finish speaking today since now even the com was interrupting! But then, when did it not?

_"Atlantis, this is the **Odyssey**, requesting permission to land."_

Make that three days late and the wrong ship. Just what was going on here?

"_Odyssey_, this is Dr. Weir. We weren't expecting to see you again so soon. It may take a little time to ensure the pier is clear for you. Is there a reason you made the run instead of the _Daedalus_?"

Not that she was about to complain, since no _Daedalus _meant no Colonel Steven Caldwell, the _Daedalus_ commander. The man had mellowed a bit in the year and a half since Elizabeth had first met him, allowing their relationship to reach a level of superficial friendship, but not so with John. The older colonel kept an almost vulturish watch over her second that put _her _nerves on edge, let alone _his_, which was the last thing the recovering man needed. The _Odyssey_ commander, by contrast, was so discreet the only other time he'd been here that she couldn't even remember his name. For a diplomat, that was a bit disconcerting since recalling such details was a part of his job.

"_No problem, Dr. Weir, thank you. **Daedalus** suffered an Ori attack just as they were leaving. No casualties, but the engines were damaged, so we took the run. Afraid we can't stick around longer then unloading, either._" A sudden discussion away from the com pick up, not quite intelligible. "_We do, however, have a VIP passenger who's... anxious to talk with you, so permission to transport him down?_"

Irritation, loud and clear, in that seemingly innocent request that was almost a plea. It didn't exactly bode well for the chances of continuing peace in Atlantis. Elizabeth crossed her arms, wincing as the beginnings of what promised to be a nasty headache made itself known. Damn it. Well, they'd just have to deal with it. As long as they could keep this guy out of John's hair, she'd be happy.

"Permission granted. We're in the Control Tower conference room."

"_Excellent. **Odyssey** out_."

Another Ori attack. War at home with an overwhelming enemy, war here with another, possibly two. It was days like today, not to mention staring at Kolya's smug features, that made the diplomat almost wish she'd never heard of the Stargate program. One gut punch after another lately, too. A shimmer of white light diverted her thoughts back to the here and now as their guest appeared a few feet away from her.

He was taller then she was, probably just over six feet, with salt and pepper hair still full and thick though he looked to be in his late fifties or early sixties. He had an athletic, wiry frame, dressed in business casual slacks and a blue polo shirt with the Air Force logo on it. Vivid green eyes sparkled as he flashed her a lopsided smile of welcome that had her breath catching in her throat it looked so familiar. She just hadn't seen it much this past week. This... this _couldn't_ be-

"Dr. Weir? Colonel Matt Sheppard, Air Force, retired, and now the newest presidential adviser."

A hand was held out to her greeting, which she stared at dumbly for a second before receiving an elbow in the ribs from Rodney, who'd moved to stand beside her. Mind still racing, attempting to catalog the possible implications of this potential one-man mess just dropped squarely in her lap, she gave his hand a quick shake.

"Dr. Elizabeth Weir, expedition leader. Welcome to Atlantis, Colonel Sheppard."

And that would be problem number one. This man couldn't be addressed as 'Colonel'. Even she knew enough about the military to see the confusion it could cause, but the way he'd introduced himself by rank meant he might not take too kindly to the necessity. Just now, though, the man appeared to be a bit embarrassed.

"I'm afraid I don't know the names of your senior staff or much about the situation here, Dr. Weir. In the hurry to transfer ships after the attack, my briefing books were misplaced by the crew."  
This kept getting better and better, she told herself sarcastically. His word choices in just that last sentence hinted at the man's character already. Instead of simply saying the books were lost, the colonel had made a point of blaming the crew. Could this get any worse?

That's when Rodney stepped forward.

"Ah, chief scientist and resident genius Dr. Rodney McKay. You wouldn't by any chance be related to _John _Sheppard, would you? Spiky haired fly boy with an appalling ability to land in trouble without trying and a distinct allergy to orders?"

Elizabeth allowed her features to blank into her diplomatic mask as she struggled to hide her dismay at Rodney's question. It had been a futile, wild hope that no one would ask before she had an opportunity to talk with John. The answer was in his personnel file, of course, though she noted that he'd never once mentioned the man to her. Nor had he sent or received any messages since coming to Atlantis, even when the Wraith seemed certain to take the city that first year.

The transformation in the Sheppard standing before her, however, left her almost speechless. Gone was the pleasant smile, relaxed posture, and lively eyes. Instead, he stood ram rod straight, hands clenched at his sides in white-knuckled fists, facial features now as cold and lifeless as Earth's Moon. Not that surprising, then, that the answer came in an equally cold, hard, contemptuous tone, though it instantly shot her temper to the boiling point.

"Major Sheppard _is _my son, yes, but I would prefer you not mention him around me. His actions in Afghanistan made him a disgrace to the uniform, and we haven't had any contact in the four years since by mutual agreement."

Somehow, Elizabeth doubted the mutual part very much, at least now. She'd seen the hesitation, then resigned sadness in his eyes when she'd mentioned sending videos home before the Wraith siege, noted how he made himself scarce when they were handing out the mail from the _Daedalus._ Knowing John, he didn't know how to approach this, how to heal the breach, and so he left it alone, making excuses to himself not to try. And _Major_? This guy didn't even know John had been promoted, nor that he was Atlantis' military commander!

Abrupt, hostile silence had descended on the room with Matt Sheppard's answer, faces filling with shocked anger at the judgmental brush-off of their friend and colleague. For a brief moment, the normally unflappable diplomat allowed herself to contemplate opening the Stargate to Earth and letting Ronon see how hard he could toss the man through. She'd bet on the former officer hitting the Control Room window, or possibly the briefing room above that. If it weren't for the politics involved... From the corner of her eye, she noted Rodney still staring open mouthed at their guest, eyes wide, face slowly tinging red, eruption imminent. Good. She had absolutely no desire to intervene and try cooling him down when the scientist would most likely give voice to all manner of rude things she _wished_ she could say. A deep breath and he was off.

"Disgrace?! _Disgrace?!_" Everyone winced as McKay's voice hit high pitch and volume simultaneously, most likely audible all the way to the Mainland. "How could you- I can't believe- You're a real _idiot_, you know that? I'm glad I'm not American if _this_ is who your president chooses as a new adviser! Sheppard is worth _ten _of you! You-"

_Beep, beep._

The com again, and a general announcement by the way Rodney had cut off so fast in mid-rant. The words sent a flash of pure fear, icy cold, race down her spine.

"Emergency teams to Colonel Sheppard's office!"

Ronon and Carson were both partially out the door before the call even finished, Rodney and Teyla a split second behind. Elizabeth was rooted in place for a long moment before hurrying to catch up, leaving their suddenly very unwelcome guest staring after them in utter confusion. Not that any of them cared to stop and explain since they were completely focused on what trouble _John _Sheppard could have gotten himself into while on base.

Especially when the voice over the com hadn't been his.

A/N: I realize that several people have been fiddling around with John's back story and parents lately, but I couldn't resist my own take on the whole thing. Especially when the official sites I've read imply that his father is still alive. Now, just what has our favorite colonel gotten himself into this time? Answers and plenty of twists headed your way!


	4. Ch 3: A Time to Fear

Disclaimer: Stargate: Atlantis and all characters therein are the property of MGM. This story is for entertainment only and the author is in no way profiting from it, nor exercising any claims to Stargate Atlantis.

Title: A Time to Heal

Author: Pyrodragon2006

A/N: Thanks so much to all of you who have been reading and reviewing! My internet has been incredibly slow due to unforeseen circumstances, so I haven't been able to reply to each of you, but thank you, thank you, thank you... Now the fun really begins!

Chapter 3: A Time to Fear

"Colonel!"

A hard shake of his shoulder, a familiar voice in his ear, both drawing him back to consciousness. Attempting to open his eyes resulted in sparkles of light, like fireflies, dancing through his vision, bringing with them a spinning sensation. John quickly squeezed his eyes shut again, completely losing all equilibrium as his stomach joined the party as well. Hands grabbed at and held him, probably saving him from a rather embarrassing face to face with the floor.

"Easy, son, we've got you. Just ride it out."

The comforting Scottish brogue helped to ground him and he was able to let the waves wash through, keeping still until they finally began to subside. Gradually becoming more alert, he realized he was seated with his back to one of the city's smooth walls, hands braced on the floor as if the environment around him were actually rocking. Something covered his nose and mouth, edges rubbing uncomfortably against his cheeks. He assumed at first that it was an oxygen mask, then noted the lack of the familiar gas brushing his face and the crinkling sound of heavy plastic just below his chin. Cautiously reopening his eyes, the colonel was grateful to find everything staying steady, if fuzzy, even when he eased his hands from the floor. Someone knelt just in front of him, one hand on his shoulder, one checking John's pulse at the carotid artery at the neck, so he concluded it must be Beckett. He reached up hesitantly for the mask only to have his wrist grabbed and restrained while he blinked his eyes rapidly, struggling to clear his sight.

"Easy, colonel. That's a re breather mask, you were hyperventilating. You're goin' to be just fine."

The Scot's features finally swam into focus, kneeling in front of him, with Elizabeth off to the side, still holding down his hand. Behind them, a grim Major Lorne, Sheppard's second-in-command, stood watching. What were they doing here? He was late for the meeting, wasn't he? Conscious of his breathing, now, he forced himself to slow down, quit panting, stop his heart from pounding wildly in his ears.

"Good, colonel, that's excellent..."

After a few minutes, Carson carefully removed the mask from his face, John gratefully rubbing at the spots it had poked into.

"Doc? What happened? I was going to get the files..."

John trailed off uncertainly, noting the activity behind his friends, especially the marines coming out of his office in full gear. Several feet away, an emergency medical team stood clustered around a gurney, talking quietly. Rather then answering, the physician began a careful examination, which John forced himself to endure, too exhausted to object, though it was a clear stall on the part of the doc. Then memory kicked in and he was frantically batting away Carson's hands while attempting to get to his feet.

"My office! There was an iratus bug-!"

Multiple hands grabbing, holding, stopping him.

"Colonel! I need you to stay down, son! Every thing's fine, just let me look at you!"

The doctor was in his face, hands back on his shoulders, while the colonel was intent on getting around him, entirely focused on the open door to his office. For a moment, it seemed there would be a potentially ugly battle of wills, then Elizabeth stepped in.

"All right, John, that's enough! Sit back down and I'll have Major Lorne explain while Carson finishes checking you."

One look at her clenched jaw and flashing green eyes told him she didn't intend to be argued with, but there was no way John was letting himself be that easily placated. Not this time.

"If that thing is still alive-"

Lorne immediately shook his head, every movement telegraphing extreme anger.

"It was a model, sir. Incredibly detailed, life-like, but just a model. Almost filled it full of holes myself before I realized it wasn't moving. You're still recovering, must have thrown your aim off. Sergeant Kirov has it."

Now John did allow himself to be pushed back to the wall, but still stubbornly resisted sitting back down.

"A model?! Why would _anybody..._"

He trailed off, getting more pissed the longer he thought about it. If he ever caught who left the thing, they'd be very lucky if he didn't introduce them to a real one. Except the idea of going near enough to one of their planets to carry out such a revenge sent a shudder through him, cold sweat breaking out on his forehead.

"I want to see it!"

Lorne winced at his superior's flat statement while Elizabeth blanched. Carson just shook his head even as John's anger went up another notch, overriding his fear. He _needed_ to see the thing for himself, to be sure.

"Colonel, I think that's a bloody bad idea."

"No, John."

His friends echoed each other in their veto even as the object of their concern tensed, determination settling over his features.

"Now, Major!"

John barked harshly even as part of him noted with mild amusement that being on the wrong side of all those superiors over the years had an unforeseen benefit. He'd known just what tone to take to have Lorne turned around seeking out Kirov before he'd even fully processed what his CO had just ordered him to do. The doctors just stared at him, identical purse lipped disapproving expressions on their faces, but he really didn't care. The safety of Atlantis had to come before anything else, or at least that was the way his conscious mind was rationalizing it.

Unfortunately, his subconscious mind had other ideas. As Lorne returned with the young sergeant in tow, John felt his mouth go dry, then powerful shudders wracked his body uncontrollably. He heard Carson swear softly and held out a hand to prevent the physician butting in, just now registering the absence of his team. He needed them here. No running, he sternly lectured himself, gaze locked on a shape straight out of his nightmares being casually held in the soldier's hands. Lorne's eyes narrowed as he raked the other officer with an assessing glance then stopped the sergeant several feet from the colonel. Deliberately, he stepped between John and Kirov, blocking sight of the iratus bug.

"Sir, are you sure?"

John barely heard the question through his heart pounding in his head. A light touch to the arm caused him to flinch back, hard.

"John, why don't we wait a minute, get your team out here. They're just in going over your office."

Elizabeth's tone made it more a plea than a suggestion, at least telling him where the rest of his friends were, but he wouldn't be put off. His focus quickly tunneled once again, the bug all that mattered even as he continued to stare at the spot where the creature would be were Lorne not in the way. One hand went down to rest on his side arm, only to meet an empty holster as he waved his second to one side.

"I have your weapon, sir. You were still trying to shoot with an empty clip when I-"

A faint flapping buzz. A yelp of absolute shock and horror. Both were out of John's worst nightmares associated with the ugly black over-sized tick now scurrying across the floor. Soldiers and civilians scrambled away from the thing, panicked shouts calling for someone to kill it. Several nine millimeters were out, but no one dared shoot and risk a potentially deadly ricochet in the full hallway, some part of John absently noted. So many to choose from, a glutinous feast for an iratus bug. He felt as if he were being torn apart even as he was unable the move, feet seemingly bolted to the floor, heart once again beating wildly in his ears.

_Kill it, run, SOMETHING!_

Vision started to gray out as his lungs tightened, forcing John to struggle for every breath. The bug paused a few feet in front of him, then lept into the air, having chosen its target- Elizabeth, standing frozen in shock just to John's right. He didn't even think, just reacted as his military mindset took over, giving the woman a firm shove that sent her sprawling to the corridor floor leaving John in the direct path of the insect. He quickly brought his left arm up in an instinctual move to bat the thing away, protect his face, the impact jolting all the way up his shoulder. Four sharp claws dug into his arm as the thing latched on, bringing tears of agony and fear to his eyes.

Then- the thing let loose, flesh tearing, and the momentum of its victim's still swinging arm sent it flying down the empty side of the corridor. A familiar whine, a red bolt of energy, and the iratus exploded mid-air, literally splattering everyone nearby with bug pieces.

John had already sunk to his knees, legs suddenly unwilling to support him. He barely felt himself hit with instectal splatter, only heard part of the loud discussion that followed.

"Eew! That's just- I think I'm gonna be sick! Thank you for that, Ronon! Geez, you couldn't-"

"You're alive, McKay, quit whining."

Sheppard felt his lips twitch ever so slightly at that, wishing he had the strength to turn and get a good look at Rodney's face.

"Yes, yes, and not so incidentally dripping with the bodily fluids of a-" Anger turned to panicked sputtering. "Bodily-! Do you have any idea how many diseases insects carry?! Where are the decontamination showers?! And... blood? I'm not- Sheppard!"

He jerked at McKay's shout, pain shooting through his body, his vision darkening. People began yelling all around him, hands again... Why were they constantly grabbing at him today? Then, blessed darkness pulled him in, quiet, wiping out the cacophony of voices even as his body fell the rest of the way to Atlantis' hard floor, landing in a pool of warm, wet liquid.

Tbc... I never said the old enemy had to be human... _blinks innocently_, I'm typing as fast as possible, I swear...


	5. Ch 4: A Time to Mend

Disclaimer: Stargate: Atlantis and all characters therein are the property of MGM. This story is for entertainment only and the author is in no way profiting from it, nor exercising any claims to Stargate Atlantis.

Title: A Time to Heal

Author: Pyrodragon2006

A/N: Wow! What a tremendous response to my last chapter! Just for that, an update without a real cliffie at the end and faster then I'd planned, though short. I hope it clears up some of the confusion many of you expressed about John's buggy visitor. Thank you all so much, and please review! It really helps!!!

Chapter 4: A Time to Mend

Elizabeth groaned as an elbow dug into her side, whoever was on top of her swearing softly in Gaelic. She'd barely had a chance to register the bug moving toward her when she'd been shoved to the side, _hard_, going down in a tangle of multiple bodies. That thing had been fake! Hadn't it? A boot on her shin had her struggling to push the others off, trying to get to her feet. Nearby, she could hear Rodney's loud complaints and prepared to chew him out as she stood and turned, finally getting a good look at the man. The rebuke was bit back at what she saw. The scientist was standing there covered from head to toe in some kind of yellowish brown goo. A laugh was bubbling up, at least until Rodney mentioned blood.

Her eyes followed those of the astrophysicist straight to her military commander, kneeling on the floor with blood running in a scarlet cascade down his left arm. Elizabeth could see the sleeve of his jacket was shredded, the flesh mangled underneath, sending a bolt of pure panic through the diplomat. John had already begun to sway precariously, face a shocking ghost white against his black hair, then his body went completely limp, dropping toward the floor. Lorne had tried to grab him, but missed, only to be pushed roughly aside by a still swearing Carson.

It had taken the physician just one look to know they had a serious problem on their hands. Heedless of the blood, which was a disturbing bright red, he knelt by the now unconscious man, easing aside the torn fabric to slap a pressure bandage on the wound. The moment he touched John's arm, however, a spurt of blood fountained out, catching the doctor across the face, then slackening off, only to jet back up a moment later. Artery, just as he'd feared. Foregoing any attempt at a bandage for the present, he instead sought out the pressure point just above the colonel's elbow, clamping the artery hard against the bone. Brigit, one of the best emergency response nurses he had, appeared next to him, efficiently wrapping the wounded limb to keep a steady pressure on the wound. Other hands slipped an oxygen mask onto John's face, a pulse-ox clip onto a finger, and an IV into the back of his right hand, them the colonel was being lifted to a gurney, careful to make sure Brigit and Carson could maintain their respective positions. They all knew the consequences if they took too long. If the artery wasn't repaired immediately, John would either bleed to death in front of them or lose function in the limb as blood flow was cut off for too long.

Wasting no time, they took off for the infirmary at a run, Carson actually straddling the injured man atop the gurney to maintain pressure. Not surprisingly, Rodney, Elizabeth, and Teyla were trailing just behind with several others, including, Carson's heart sank, Matt Sheppard. Where was Ronon? A bellow from ahead answered that one, the Satedan obviously having taken it on himself to ensure a clear path through Atlantis' corridors. It might only gain them a few seconds, but... It could make all the difference.

It never ceased to amaze Carson how lucky Colonel Sheppard really was. The man had survived time after time when the physician was certain his friend was dead, usually with only minor injuries to boot. Now, though... to have the man's luck run out while on base, just going to his office to retrieve some bloody files after what he had miraculously been saved from only days before... It wasn't bloody fair.

The infirmary, none too soon, his second, Dr. Bethany Kirran, waiting ready at the door. He breathed a slight sigh of relief at the sight, since the woman hadn't been on duty. There was no one he'd rather have assisting him at the moment. The grandmotherly doctor in her fifties had already paid her dues in field hospitals during the first Gulf War as well as all the isolated hot spots of the 1980s- Honduras, Panama, Israel, and too many others. This type of injury and the turn on a dime treatment needed was no stranger to her, unlike some of the other buffoons Carson had looked over the files of.

"The surgical suite is ready for you, Alexa and Karl assisting. I'll handle your followers, then be in myself."

"Excellent. Thank you, love."

Those pushing the gurney didn't even break stride, whipping on past even as Carson answered the other doctor. Pulling to a stop just outside the surgical area, Karl Thompson appeared to take over Carson's position, allowing the doctor to slip to the floor. The gurney carrying his patient continued on while two nurses descended on him, prepping him with a surgical gown, cap, and gloves even as he scrubbed up. Inside, he knew there would be an equally rapid preparation of John.

Once in the surgical theater, it was all business. Find the tear in the artery caused by the iratus, figure out how to close it, and return circulation to the limb as soon as possible. If the lad's luck held, it would be small enough to be sutured shut with special thread that the body could absorb as it healed. If not... The Scot sternly told himself not to dwell on the potential difficulties of an arterial graft. Bad enough to face that if it happened. Quickly, Carson turned his attention to the units of plasma and antibiotics being hung with a nod of approval, then checked the stability of his patient. Dr. Shang, the anesthesiologist, had already intubated, giving his boss a quick thumbs up. The colonel's vitals were stable for the moment, though right on the edge of critical, so they had no time to waste.

"All right, let's see how severe the damage is. Alexa, make sure those wounds are well irrigated, we have no bloody idea what nasties those bugs could carry. Karl, you'll be assistin' me with suturing until Bethany gets in here. She's doin' a quick check of the others and sending them to decontamination."

A busy quiet descended on the room, the loudest noise the thankfully steady beep of the heart monitor. It didn't take long to locate the source of the arterial blood and Carson didn't bother holding back a sigh of relief at seeing only a small tear, easily handled. That dealt with, they moved on to the raking gashes from elbow to wrist left behind by the bug's claw like legs. The work was grim, quiet, as they struggled to piece together shredded skin and partially ripped muscle, broken only by Carson's soft requests for tools, sponges, or further suction. At least, until the door opened and a furiously muttering Bethany stomped in.

While the older physician began clean up on another gash without a word, the others traded wondering glances. Normally, it took an act of extreme stupidity to put the relatively even tempered doctor into a snit, and none of them had seen her as bad as this. Bethany's anger tended to be loud and short, not the simmering wordless fury they were being presented with now. Work continued for several tense minutes, no one willing to breach the silence and risk being the innocent target of the woman's coming tirade. Finally, Carson sighed, deciding rank had its downfalls.

"What's wrong, Bethany-love?"

Stormy gray eyes snapped at him.

"An iratus bug, Carson?! On _his desk_?!"

The Scot winced at the volume, but definitely agreed with the outrage. Colonel Sheppard's previous encounter with one of the things was fairly common knowledge around Atlantis, as was his insistence the incident never be mentioned around him.

"Aye. Suture- ah, perfect, Karl. Alexa, keep a steady eye on those vitals. Bloody thing didn't move for a while, who knows why, maybe hibernation, so they thought it was one of the new models the xenobiology lab ordered. Then the thing starts buzzin' and went for Elizabeth. Colonel Sheppard shoved her aside."

A snort. "That's our colonel, all right. So who's the south end of the north bound donkey-horse cross out there? The one who looks like an older version of John."

Uh oh. Carson could practically see the steam pouring from Bethany's ears. At this rate, the bloody fool would have over half of Atlantis after his head by nightfall, a feat even Kavanagh hadn't managed! And the ones whom he was ticking off... Well, the elder Sheppard couldn't have handpicked worse enemies in all of Atlantis.

"That would be Colonel Matt Sheppard, the new presidential adviser and our colonel's father." Carson told her sourly. "Why? What did the daft bugger say now?"

"He asked me point blank not to go to extraordinary measures to save full use of John's arm! Said our colonel and the Air Force would both be better off if they parted ways. I thought Major Lorne was going to shoot the bastard right there. Hell, if you hadn't needed me in here, _I'd _have slugged the creep!"

Carson snorted behind his mask, not too surprised, and went back to carefully checking another gash for any more torn muscle or damaged veins before putting in sutures. So far, the worst had been the artery, which appeared to be holding up nicely to the renewed blood flow. The damage to the muscle wasn't severe, just painful, and the tendons were in tact, or no amount of physical therapy would have allowed total recovery. Which, as a military officer, let alone a pilot, John needed to have. The doctor looked forward a bit sadistically to being able to give the news to a certain retired colonel waiting outside. Stupid haggis.

"I gather the colonel's team wasn't around to hear or Dr. Biro would be needed in the morgue."

A quiet laugh. "Yes... This one isn't anywhere near as deep as the others, more of a puncture. The creature's mandibles, perhaps?"

Carson turned over the suturing he was doing to Alexa and pulled one of the lights around to flood the spot in question. It was on the back of the colonel's wrist, opposite the gashes, and much smaller. Testing Bethany's theory, he carefully wiped dried blood from the skin around it, looking for an identical mark from the iratus' other mandible.

"There's the other one." He noted the puncture in dismay. "I think you might be right, love. Odd, though. If the critter really latched onto him like that..."

He trailed off as blue eyes met gray, neither one wanting to give voice to what they were thinking. News of the Wraith's words to John after restoring his life had raced through Atlantis like lightning.

"As soon as the colonel is sufficiently recovered, I'll run all the blood work again."

Tbc... Probably after the holiday. And, no, I don't know much about medicine beyond first aid training, so please be kind.


	6. Ch 5: A Time to Learn

Disclaimer: Stargate: Atlantis and all characters therein are the property of MGM. This story is for entertainment only and the author is in no way profiting from it, nor exercising any claims to Stargate Atlantis.

Title: A Time to Heal

Author: Pyrodragon2006

Chapter 5: A Time to Learn

Matt Sheppard stared after the retreating form of the petite lady doctor, teeth clenched so hard his jaw was already starting to ache. For a moment, he'd actually thought the woman was going to slug him! Truth be told, deep down Matt had a niggling suspicion that he would have deserved it. The young major sharing the waiting room with him obviously thought so, standing rigid, glaring at him, one hand resting on his sidearm. The comment hadn't been called for, really, but so many emotions were sweeping through the retired colonel that he wasn't completely sure which way was up anymore.

The officer and Matt were the only ones out of the bunch who'd followed the gurney not to be sent to the decontamination area to wash off bug bits and change clothing. The colonel had already decided the lot of them would probably set a speed record for the activity, which Matt was glad he didn't have to endure. He himself had been waiting well down the hall for whatever the crisis was to be handled while the major mentioned being behind the large man with the dreadlocks.

The very last thing that Matt had ever expected was to see John wheeled by, heavily bleeding and unconscious, arm ripped open! No wonder that arrogant scientist had immediately asked if there was a connection. Now, they were both trapped here, unable to avoid one another, at least for the next two months and Matt had no idea how either one of them would handle it. Several minutes of tense silence filled the room as the colonel paced and his companion glared. Finally, as the others filed back in, hair wet and clothes showing signs of haste, Matt stopped directly in front of the major. The soft chatter of the non-military people instantly ceased, a thick tension filling the space as the others took note of the pending confrontation.

"If you have a _problem_ with me, major, I'd like to hear it!"

They were toe to toe, the older man towering over him wearing a scowl learned from the best drill sergeant in the service, but the young major didn't even flinch. The demand from the colonel seemed to be all he was waiting for since it was phrased to give tacit permission to speak freely. Of course, Matt being retired made him technically a civilian, but for once he didn't adhere strictly to regulations.

"Yes, sir, I do. I think you're a real jerk, sir." Matt could feel his face beginning to flush red in rage, but the kid went on, seeming not to care. "That was one of the shittiest things I've ever had the misfortune to hear from _anyone_, let alone a military officer, and about your own _son!_"

Now _that _was a bucket full of icy cold water to his hot anger! He took a step back, both physically and mentally, realizing the major had a point.

"You're right, major. That _was _completely inappropriate, no matter how angry I am with John. I ask that you disregard it as a result of shock and stupidity. I had no idea Major Sheppard was here until the medical team brought him past."

If he hadn't been still feeling so out of control and pissed, he'd have enjoyed the flabbergasted looks from Weir and her bunch. Right now, though, he had another issue to deal with since even having permission to speak freely only went so far. Even when the younger officer was right.

"I think, major, that I-"

The kid actually had the gall to cut him off!

"If you want to report me, go right ahead. I'm Major Lorne and my superior is Atlantis' military commander, not to mention one of the finest officers its ever been my privilege to serve under, Lieutenant Colonel John Sheppard."

It took a moment for what Lorne had said to sink in, then Matt found himself staring in utter shock. What the hell was going on here? His son had been promoted _and _given his own command after the career ender he'd pulled in Afghanistan? Someone must have really had the brass over a barrel for that to happen! With an angry mutter, he slammed a fist into the wall, ignoring the glares of the others, not to mention the low growl coming from the large man. Growling! What kind of a crazy world had he found himself on, anyway?

Matt had been contentedly enjoying his retirement, working on a memoir of a Cold Warrior, almost guaranteed to sell well given his status as a hero and Medal of Honor recipient. Then his phone rang, an old friend on the other end, Henry Hayes, asking him to serve as a special military adviser to the president. Less than twenty-four hours later, he'd been informed that the United States had been fielding units to other planets and working with aliens for ten years now (Why, oh why didn't some of them wear clothes?). Oh, and not so incidentally, the whole thing was headed by one of the most maverick officers he'd ever had the misfortune to cross paths with, Jack O'Neill, now a Major General. While Matt himself had never managed to rise past bird colonel despite being a genuine American hero! Then he'd been thrown onto _spaceship _(How come he hadn't known the Air Force had such a thing?!) bound for another _galaxy_ (Were they serious?!) when the damned thing got attacked by aliens! And _where_, exactly, was he going? The fabled lost city of Atlantis, which really had sunk, but, oops, wrong planet!

Now, to find the young man who he had sworn he would have nothing more to do with, here, hurt... To say Matt's stomach was filled with butterflies would be a vast understatement. For once in his life, he didn't know what to do, how to react. Once again, Dr. McKay stepped in to fill the void, matching him glare for glare.

"I don't know what you just said, but judging by Lorne's reaction, I'm guessing you must have shared more of the stellarly poor opinions you communicated in the conference room. As personally satisfying as it would be for me to see Ronon rip your head off after Teyla kicks the rest of you black and blue-" The scientist gestured to the large man and petite woman with him, both clearly furious. "I feel we owe it to Sheppard to warn you that we're his team. Our tolerance level of idiots making nasty comments about our team leader and friend is at an all time low right now, so you might want to curb that or you'll need new teeth. Or, in terms your limited intelligence can understand- Shut up!"

"Rodney! That's enough!"

Elizabeth Weir's sharp rebuke didn't quite sound completely sincere to Matt's ears. Also, he'd noted the expedition leader waited until the end of the man's tirade before saying anything. Fine, he could play their game. It wasn't surprising, really, for civilians to defend John, since few of them would have even the faintest understanding of how the military functioned. No, what kept his anger simmering was the defiance of the young major. Either he hadn't heard what happened in Afghanistan, which would be unlikely given the Air Force rumor mill, or he was just as much a misfit as John or O'Neill. Great. What the hell was he doing here?

"I'll ignore that because emotions are running a little hot right now, _doctor_." The retired colonel smiled coldly as he managed to twist the title into a questioning insult. "Especially seeing as how I doubt your precious colonel bothered to tell you about the fatal mistakes he made while serving in Afghanistan. Only fatal for others who trusted John, of course."

This time it was McKay who blanched, letting Matt know he'd hit his bull's eye. Just maybe it would shut the man up for a while. Weir, however, was examining him down her nose as if he were some slimy creature she'd just found under a rock.

"I've read the report on what happened. Try again, _Mister_ Sheppard."

The 'mister' set him to bristling, but he wasn't about to allow her to distract him from the issue at hand.

"Reports rarely tell the whole story, doctor. I-"

"Are the lot of you quite through tryin' to put more patients in my infirmary?"

The voice from behind him, an exasperated thick Scottish brogue, brought him around in surprise. In the doorway, surgical scrubs still spotted with blood, stood a very unhappy, exhausted looking physician.

"Carson?"

Interesting. Dr. McKay's tone had gone from very sure of himself to hesitant, almost scared when he addressed the Scot. A feeling Matt, as unwilling as he was to acknowledge it, found echoed in his own heart. He braced himself for the news he'd feared so long, anger abruptly vanishing as if it had never been, his apprehension copied on all the others' faces in the room. Then the doctor flashed a reassuring smile and the body postures of those around him relaxed somewhat, and Matt's irritation returned full force.

"He should be fine with a little time and rest. The iratus bug apparently latched on hard to his forearm, resulting in four deep lacerations and some tearing when the legs were wrenched loose. One of them nicked an artery, but we caught it quickly, before he lost too much blood. He'll be a mite bit sore for a while, and need a little physical therapy, but barring complications, everything should heal nicely. The real puzzle, though, is two minor punctures Bethany found."

"Well, if they're minor, then why-"

"If you let me bloody well finish, Rodney, I'd explain it!" The doctor's sharp words and raised voice caught everyone by surprise, causing Carson to flush. "Sorry." He ducked his head, then seemed to return to 'doctor' mode. "The wounds are, at a guess, from the critter's mandibles."

Blank looks all around, including from Matt. Biology had never been his best subject, but if he remembered correctly, then the man was saying the bug-

"It bit him? Why is that strange?"

The moment he spoke, the temperature in the room approached Arctic. At least, that's the way Matt felt with the reception his question got. He allowed some heat to fill his own glaze in response. Battle lines were clearly being drawn.

"Aye, the biting part isn't that odd. The problem is these bugs aren't known for lettin' go once they grab onto someone. The beastie only went flyin' down that corridor because _it_ wanted to, and we don't know why."

"Great. Just what we need right now, another problem centering on Sheppard!"

Matt suppressed a soft chuckle. Dr. McKay's mercurial moods were rather entertaining to watch now that they were no longer aimed at _him_. He just hoped he had the opportunity to get the man into a poker game, relieve him of all his money. The man couldn't have a poker face worth speaking of! At the uncomprehending looks around the scientist, the expressive genius rolled his eyes with a put upon 'why must I deal with imbeciles?' sigh.

"One, why did the thing let go of Sheppard? Two, how did it get in his office, or on Atlantis for that matter? Can we see the colonel now, or do you have more voodoo up your sleeve, Carson?"

Even Matt fell silent as the possible implications of a dangerous creature being brought the city secretly was contemplated. The sober mood told him just how serious this whole thing must be, whatever the hell an iratus bug was. Meanwhile, the physician had frowned at McKay's request, but surprised Matt when he gave a short nod of agreement.

"Fine, seeing as its probably the only way I'll get the lot of you out of here."

With that, Beckett led them through what seemed an utter maze to Matt, completely unlike any other infirmary the colonel had ever been in. He saw isolated areas with strange equipment, research labs, a storage area, then one larger room with several beds, two occupied, but they continued on. Instead, the Scot went past another lab and office area, finally halting near a door in the very back of the complex. Matt frowned in puzzlement, but a quick glance showed none of the others seemed to think this unusual. Beckett began to lift a hand to trigger the door, then paused, turning to face them, a stern expression warning not to push him as he met the eyes of each in turn, clearly the master of this domain. All except Matt, that is, who found himself on the receiving end of a hostile glare, clearly in hot water already. He grimaced in return, reminded once again of how much he hated anything to do with doctors.

"He's still under sedation, so only a brief moment."

With that last firm stipulation, the door slid open to reveal a still form on the bed surrounded by machines.

_Beeping, blinking, whooshing, invasive tubes, IV, monitors..._

Stomach lurching and head spinning, Matt backed out fast, forcing Dr. Weir and Major Lorne to hastily sidestep out of the way. Before a word could be said, the colonel allowed his face to harden into that of a dismissive superior officer, not someone many would dare to question. The others, however, merely gifted him with varying degrees of contemptuous stares as they went silently around him. As soon as the door closed behind them, he collapsed against the wall, slight tremors racking him as he fought the memories and the pain that inevitably came with them.

Iron control slipped back into place just in time as the others filed back out, most not bothering to hide their disgust at what the elder colonel was certain they saw as a brush-off. Not that he gave a damn, since his past and his relationship, or lack of one, with the man in that room was none of their business. John's team was sharing significant glances, obviously communicating without a word in a way only the best displayed, because Dr. McKay nodded as did the petite woman, Teyla. Then all three turned to Major Lorne and Dr. Weir.

"I'll stay with Sheppard tonight while McKay and Teyla start the investigation."

Ronon wasn't asking, apparently taking for granted his right to decide though the man clearly wasn't US military. Matt felt himself bristling in anger, waiting for the rebuke to come, but neither Weir nor Lorne seemed the least surprised. In fact, they looked a bit relieved!

"I can assign people to guard the colonel, Ronon. Or at least someone to give you a break."

Lorne's offer was met with a simple head shake from the large man while his petite team mate answered quietly.

"Thank you, major, but until the source for the iratus bug is discovered, we prefer the team watch over John. After recent events, he is unlikely to be comfortable with those not very well known to him."

A snort of veiled amusement from McKay.

"Speaking of recent events, I can't wait to see his face at the wreck he made of his office! Not only are there bullet holes everywhere, but he _missed_!"

Matt clenched his jaw at the scientist's jab at John, hands curling into tight fists at his sides, though he wasn't quite sure why he cared so much. A glance to the side revealed his annoyance reflected on the young major's face as well. No matter what, the colonel decided, his feelings were about John being in the military or his past choices, no one was allowed to make remarks like that about one of the finest small arms marksman Matt had ever seen. There was simply no way the lieutenant colonel could have missed! Expecting that perhaps he'd find himself backed up on this one by the rest of John's team, he turned to Teyla and Ronon, but there was no irritation there. Both were shaking their heads with slightly patronizing smiles for their weapons' ignorant team mate.

"He didn't miss, McKay. The shots all went straight through, the bug just healed that fast."

Not waiting for the stunned astrophysicist to reply, Ronon turned and slipped back into John's room.

"Aye, and you'll not be throwin' _anything_ about this in his face, Rodney! He's barely begun his recovery and now he's had another, older trauma piled on top!"

The other man hastily backpedaled from the sputtering Scot, shock turning to anger, then outrage on his face.

"Of course not! I meant- well, just- I wouldn't say anything until he was able to take it, you know that. Anyway, he's never let me forget blowing up half a solar system!"

"**Five-sixths!"**

Several people spoke at once in good natured exasperation, even as Matt gaped at the man, fervently hoping it was some sort of bad joke. Weir apparently noted the confusion, but before she could say anything, Beckett continued.

"I'm afraid the trauma is the part that worries me the most. The colonel hyperventilated an' passed out in his office just before you found him, major. I'd like to speak more about it with the colonel first, but I may need to meet with all of you soon."

"John did _what?!_"

Matt exclaimed in shocked contempt as he stared at the doctor. The other man narrowed his eyes at him, angry, but didn't bother repeating with he'd just said. The colonel shook his head, giving an annoyed snort. The boy had always been too soft, in his opinion, too caring for the military. It was the part he'd gotten from Matt's second wife, John's mother, Heather. Combine that with Matt's bullheadedness and John's own unique maverick streak, and it spelled disaster of epic proportions in a military setting. This just proved it. Soldiers didn't _faint_, especially from finding an overgrown insect in their office! This was the person trusted with the military command of Earth's farthest outpost? What happened if they came up against a truly tough adversary, such as the Ori the _Odyssey_ crew had told him about?

Dr. Weir was watching him, green eyes flashing angry warning signs not to say anything further. He hated diplomats! They were the only people he'd ever encountered as a group who could read his body language so fully and accurately. It simply wasn't natural! Then, many of them couldn't stand the military, either. Instead of saying anything to him, however, she turned to the Canadian.

"Rodney, please go load the relative reports and recordings onto a tablet for our uninvited guest. You know which ones, all of them, including the accompanying medical. Before Mister Sheppard digs his hole any farther toward the planet's core!"

He really could find himself hating that woman.

"That's _Colonel _Sheppard, doctor!"

A soft, rude noise caught Matt's attention as he and Weir stared each other down and he turned, ready to lay into the major.

"With all due respect, sir," As Lorne began, Matt wished just once that he could hear the phrase uttered with something other than contempt or anger! "You're retired. Chain of command protocols clearly indicate that only Lieutenant Colonel Sheppard be addressed by his rank in such a situation to avoid any potential confusion."

_That _was a pin deflating his ego in short order!

"Fine. You're correct, major." Matt finally bit out.

A nod and they spent several minutes silently waiting, no one willing to try starting another conversation. Finally, Dr. McKay reappeared, shoving a tablet PC into the older man's hands along with a white envelope.

"You know how to use one of these, I assume. Don't leave it anywhere, some of those reports are highly classified even for Atlantis personnel. The letter some airman from the _Odyssey_ gave me, apparently under the mistaken impression that I have nothing better to do then deliver mail to you."

Matt bit his tongue to keep from retorting to that one. Old soldier or not, he recognized when it was time to retreat. He grabbed both items and headed out, grateful to discover a map of the relevant part of the city called up on the tablet. Now all he needed was a private place to think.

TBC...


	7. Ch 6: A Time to Listen

Disclaimer: Stargate: Atlantis and all characters therein are the property of MGM. This story is for entertainment only and the author is in no way profiting from it, nor exercising any claims to Stargate Atlantis.

Title: A Time to Heal

Author: Pyrodragon2006

A/N: Thank you so much to all my reviewers!! Wow! Fanfic just dropped a ton of them into my e-mail finally! Sorry for the short delay on this chapter, I will try to adhere to a schedule of at least one update a week from now on!

Chapter 6: A Time to Listen

Elizabeth watched John's father retreat without a word, still unable to get over the sheer gall of the man. Ass didn't even begin to cover it! As a diplomat, she had long prided herself on her ability to maintain an open mind, carefully masking any personal judgments about the participants, but with Matt Sheppard, that distance eluded her. After only a few hours with the man, she was more than ready to see the backside of him. Preferably to kick it. So much for her rule of no threats of bodily harm! How John could be related to him boggled the mind.

In every way she'd seen so far, Matt was the antithesis of his son. Where John was considerate and modest, almost to a fault, Matt was rude, superior, arrogant, and unwilling to change his set views in the slightest. The son was flexible to the point of throwing out the rule book completely while the father lived by it. Almost instantly upon meeting someone, John was able to put them at ease. The elder Sheppard effortlessly antagonized. The contrasts were staggering.

"Well, now we know why Sheppard never says anything about his family, even in passing. Who'd willingly admit to having _that _as the donor of some of their genes?"

Elizabeth had to hastily duck her head to conceal a very unprofessional smile. Trust Rodney to find the most colorful way possible to say what they'd all been thinking! A presidential adviser? Frankly, Elizabeth had credited President Hayes with more intelligence than to accept the judgment of someone like that. Of course, he'd also allowed himself to be placed on the same ticket as former Vice President Kinsey, so maybe not.

"Let me handle our guest, Rodney. You just concentrate on our bug problem with whatever resources are necessary. I want to know how that thing got into the city and why it was so still everyone thought it was a model at first. Also, make damn sure there aren't any more if you can. Major, I'm leaving all non-essential off-world missions suspended for a few days more. Keep me informed as to any progress, all of you, and Carson, please let me know when John's able to have visitors. _Someone_ is going to have to tell him about our visitor, and I think it might be best coming from me."

None of them looked ready to dispute her claim to _that _little chore. Carson grimaced, then gave the woman a sympathetic pat on the shoulder.

"We'll take good care of him, love, don't you worry. I'd almost like to see anyone try to get past Ronon right now! As for the rest, we take it one day at a time and give him all the support we can. The colonel's restin' comfortably for now."

Elizabeth winced at the doctor's emphasis on the last two words, knowing the events of the last- a glance at her watch as she began to slowly make her way out of the infirmary revealed it just going on five pm Atlantis time. Had it really only been a little under three hours? Was that even remotely possible? She had to laugh at herself for that one. With John around, the answer was always a resounding 'YES!' It seemed to be the fate of such a caring, charismatic leader to pull in trouble as fast or faster then he pulled in friends, especially in the Pegasus Galaxy. In her world, it was roughly the equivalent of being a negotiator sitting between the Palestinians and the Israelis- you were simply asking for your head to be handed to you with an ulcer thrown in for free! Granted, John's style of trouble was usually more painful not to mention potentially lethal...

"Dr. Weir! Was it truly necessary to allow Dex to shoot it? All I have left to study are parts! Look at this!"

The Atlantis leader found herself recoiling fast from both the verbal barrage and a plastic wrapped iratus leg being waved in her face. Her stomach clenched painfully in annoyance. She really should have known this would be coming. Forcing a calming breath, she met the other woman's eyes.

"Dr. Malenkov, I'm sorry but there wasn't a choice at the time. The safety of Atlantis simply had to come first. You have parts to study, which frankly is more than Colonel Sheppard and I agreed would ever be allowed-"

"Exactly! I remind you I am doing important research that could hold the key to saving many lives, and I am not even allowed a dead specimen! How can I possibly advance my work under such conditions? Twice only we have had Wraith, yet both times others were put before me, and now you destroy my bug! In Moscow-"

"You're not in Moscow, Doctor!"

Elizabeth snapped, already losing what few shreds of control she had left over her temper. The irate scientist was still brandishing the bug appendage, obviously completely oblivious to any ramifications beyond her own little world of the lab. To raise a ruckus over such 'specimens' here, now... The Atlantis leader was just thankful John was safely tucked away in the infirmary where the Russian couldn't get at him about it.

Besides, this was nothing new. The woman had been a thorn in her side since Antarctica, with a constant litany of complaints about regulations, lab space, equipment, restrictions on testing, the list went on. As soon as she wore Elizabeth down on one thing, the diplomat finally giving in just to shut her up after attempting all manner of compromises, she would find something new. For months now, it had been John's insistence on no further iratus or Wraith specimens of any kind being brought to the city. Research into the two related alien species was necessary, yes, but had been taking place only in special research facilities set up off world, and not on any live Wraith. The risk of contamination from a bug or either type of alien fooling them with hibernation was too great, according to Colonel Sheppard. After everything that had just happened with Kolya, as well as this latest mess, it wasn't an issue Elizabeth was at all ready to over rule her military commander on. She had been so certain that there couldn't be any iratus on Atlantis that it had never even occurred to her to question their immediate assumption that the thing on John's desk was one of the new models the science lab had ordered just because it hadn't shown up on a scanner. They _knew _the things didn't show when hibernating, how stupid could they get? What motive would anyone have had to do such a thing to John, even with the rumbles she'd heard in the the last several days? As for that, how could someone possibly rationalize blaming John for taking any avenue he could out of that hell-hole, even allying-

"Dr. Weir!"

Malenkov's sharp rebuke brought her attention back to the scientist and she realized the woman had been loudly bitching the entire time Elizabeth was lost in her own thoughts.

"Dr. Malenkov, Colonel Sheppard's directive will _not _be changed. We've done what we could to ensure you can do your work, but now I'm afraid you'll have to make do. And do to recent events, please inform your colleague Dr. Chen that members of Colonel Sheppard's team may need to speak with him, they're handling the investigation. Yourself, also, since you _are _our leading expert on the iratus bugs and may be able to help us track where this one came from."

For a moment, Elizabeth thought she might see actual steam pouring out of the ears of the entomologist/xenobiologist.

"You do not believe one of us would bring one here against the express orders of yourself and Colonel Sheppard?!"

Uh oh, iratus leg waved in her face again. While Elizabeth _did _harbor a few suspicions about just that, she certainly couldn't _say_ it. Besides, she wasn't sure how much was her jumping at shadows because she'd once again allowed John to be on the receiving end of a nasty situation she should have been able to prevent. The last thing she needed to do was compound the whole mess by repeating the mistake she'd made last year with Kavanagh!

"No, its just routine. You'd be the one most likely to know the signs we need to look for to trace the bug's path on Atlantis, find where it might have hidden, that type of thing. We also need to establish a time line and possible opportunities for the iratus to have hitched a ride aboard a Jumper visiting their worlds."

Dr. Malenkov silently stared at her for a long moment, and Elizabeth held her breath, afraid the woman wasn't buying the assurances.

"Fine." The Russian grimaced, locking gazes with the diplomat. "We will make our records of all such trips available and hold ourselves ready to assist in any way necessary. This will take much of our time, however, and delay our research, as does the current restriction on gate travel, so I expect we will be appropriately compensated." A pause for effect. "Or I _will_ have to make my concerns known to the IOC. I assure you, I will not be brushed off by them, as that mush-brained idiot Kavanagh was."

Malenkov turned on her heel and stalked off, leaving a gaping Elizabeth behind, trying to decide just how she should respond to such a threat. Or had it been a warning?

Matt Sheppard stood on the balcony near the infirmary, looking out over the incredible city he still wasn't quite sure he believed existed. It was so unreal, beyond anything he could have imagined, to have American servicemen and women out here, fighting alien creatures alongside soldiers from at least three other countries- Britain, Germany, and Russia. Russia! The very people he had been lauded as a hero for fighting twenty years earlier, unacknowledged by either government to the public, of course! And the beings that they fought! Something that could age you with the touch of a clawed hand? Withstand bullet wounds that would kill even a bull elephant?

The first files he'd gone through were overviews of the various major players in the Pegasus Galaxy, chief among them the Wraith. The military reports were bad enough, but the graphic medical depictions of the damage the things could do were truly horrifying, even for a soldier. Within those reports, he'd come across references and reactions to someone being tortured using a Wraith, as well as a link to three small video files. Not even the hell that had been Vietnam had prepared him for what he saw. The inhumanity, the pure agony of having one's life ripped slowly away, year by year...

He'd immediately lost his lunch over the railing like the rawest of recruits and hastily decided supper wasn't worth trying. For _John _to show that much pain... Most people he knew wouldn't have survived, he was certain of that, and those who did wouldn't have been sane. The strength, physically, mentally, and emotionally, that John had shown was incredible! No wonder everyone was so protective of the young colonel right now! Briefly, he found himself once again regretting the distance that had so abruptly come between them. The officer he was seeing in those reports showed a courage and resourcefulness he hadn't known was in his son, though the appalling disregard for the chain of command had Matt rolling his eyes. He was torn, the love of the child John had been hitting the wall of contempt Matt held for the man his son had become, though a few chinks were opening in that barrier. John's actions of four years ago, the betrayal, however, was still unforgivable. With a fist slamming the railing, his cold anger at the younger man returned, hardening his heart. There was no forgetting and forgiving, not now, not ever. Fuming, he stalked back to the small bench where the computer and letter both waited. He dismissed the former for now.

It was time to see what his friend Henry had to say for himself. After all, there was no way the man couldn't have known John was here, in a position of authority. Henry was the _president_, for cryin' out loud! Matt grimaced. Leader of his country or not, Henry Hayes could be an extremely cocky, sneaky son of a bitch when he wanted to be. 'Course, that was the definition of a politician, wasn't it? Carefully, he pulled out the envelope marked with the presidential seal, his name printed on the outside in his friend's distinctive hand, along with a note that it wasn't to be delivered until they reached Atlantis. Inside was a single page, hand written.

_Matt,_

_By the time you get this, you'll probably be pretty upset with me. The only defense I have is that you need to face this- both of you- before all you have left are regrets. That kid of yours has been doing one hell of a good job out there despite the odds he's faced. I know you swore never to acknowledge John again after the rescue fiasco, but I also know you said that in the face of terrible pain and anger, losing Melissa then Heather the way you did. You've had four years to cool down, my friend, but time doesn't seem to be helping, so I decided it was time to take a hand. Matt, please, just sit down and talk to your son. According to Dr. Weir and Generals O'Neill and Landry, John's turned into a fine leader._

_I really do want you to advise me on the Stargate program, so you'd better be paying attention while you're there. Though I must say, getting attacked before you ever leave the galaxy is not the start I'd hoped for! Guess the Sheppard ability to attract trouble is working overtime! Try not to let it get both you and John killed._

_I'll see you on your return home, even if it means a punch in the jaw. Please, take the time to listen to those who've worked with your son the last several years. Give yourself and John a second chance._

_Julia sends her love._

_Henry_

_PS... You'll find an extra case when you unpack. Guess your briefing books made the transfer after all._

_PSS... Don't forget I know who taught John Sheppard half the tricks he's been pulling out there. Do yourself a favor and pull your head out of your ass._

Matt groaned, flipping the letter over onto the seat. He should have known Henry was up to something when those books disappeared before he had a chance to look at them! Though, come to think of it, the letter had obviously been written after the attack on the _Daedalus_, so how had Henry planned on originally pulling it off? Not that it mattered as amusement at his friend's high handedness turned to anger. The meddling, as well meaning as it was, stabbed deep. To force John and Matt into each others' laps... Henry wouldn't be enjoying the discussion when he returned to Earth, that was for sure.

"Damn you, you white toothed manipulative jackass! You know how much I hate not being in control?!"

His fierce muttering went on for several minutes, using the most colorful expressions he'd picked up from a lifetime in the barracks. Finally, rage gave way to determined resignation. Fine. He'd simply ignore the ulterior motive and abide strictly by the official reason he'd been sent here. Colonel Matt Sheppard, retired, would learn what he could about Atlantis, then return home to advise his president. To start off, it would be helpful to review the rest of the mission logs from Lt. Colonel Sheppard's team.

Matt swung around on the bench- only to see a human shape come barreling out of the shadows by the wall, headed straight for him. With a gasp, he stood, reaching for the weapon he no longer carried even as he kicked at the bench, hoping to knock it into his attacker's path. No such luck as the other man leaped it easily. Stupid, stupid, stupid! Now the colonel was pinned against the railing, unable to do anything more than raise his arms in a last ditch defense. The two collided with bone jarring force, momentum sending them flying over the railing toward the water below. This wouldn't be a pleasant landing. A second later, they hit, shock driving precious air from his lungs, the right side of his body feeling as if it had been stabbed by a thousand tiny knives. Abruptly numbed hands lost their grip on his opponent as he sank deep into the dark, icy cold water, leaving him in a fight for his life against a second relentless adversary- nature.

Burning lungs urged him to breath, though it meant certain death, but he was no longer sure which way was up. It took all his concentration and control to release only a few bubbles of air from his lungs. They just brushed his left hand, and he quickly righted himself in the water, kicking hard for the surface, cursing the heavy drag of wet clothing and the strength sapping temperature of the alien ocean. He was almost to the point of taking that fatal watery breath when his head broke the surface into air rapidly cooling with the onset of night. Breath after breath, sweet, clean, never before so welcome. His teeth instantly began to chatter and his limbs took some stern convincing to begin a standard treading motion.

It was only as he allowed himself to rest a moment that the absence of his assailant anywhere around registered. Hopefully, that meant the other man- and he was sure it was a man, the build was distinctive- had drowned. The ocean around him was calm, reflecting the spectacular yellows, oranges, and pinks as the sun touched the horizon, heralding the coming darkness. Not to mention adding to his problems. He was dismayed to note the city was farther away than it should have been... and the distance was growing.

"Shit!" With a snort of annoyance, he slapped the water, earning a plume of it straight into his own face for the trouble. "Must have landed square in a current!"

Sheppard was a strong swimmer, but even an Olympic record holder would have little chance of reaching the city under these conditions. Even without the current pulling him away, the cold would sap his strength and dull his mind. Then, if by some miracle he reached Atlantis, he had no idea if there was a place to access it from the ocean or even how to call-

"Wait a minute! The com!"

He'd been issued one of the small devices earlier in the day! If by some chance it had stayed in his ear through the fight and ducking... Fearing it was too much to hope for, Matt reached one shaking hand to his ear, then let out a moan of sheer relief at feeling the thing still there. Now, if it worked, he might just get out of this mess alive. Hesitantly, he tapped the com.

"Matt Sheppard to Atlantis, I am in the water. Repeat, I have been attacked and am in the water, please send rescue! At-!"

Something or someone firmly grabbed his leg, yanking him under the water.

TBC...

A/N: Now, what has the Sheppard luck gotten them into this time?


	8. Ch 7: A Time to Give Thanks

Disclaimer: Stargate: Atlantis and all characters therein are the property of MGM. This story is for entertainment only and the author is in no way profiting from it, nor exercising any claims to Stargate Atlantis.

Title: A Time to Heal

Author: Pyrodragon2006

Chapter 7: A Time to Give Thanks

Elizabeth briskly made her way toward the Control Room, wondering what else could have _possibly_ gone wrong. She had been enjoying a late evening meal in the company of Teyla, Rodney, and Major Lorne, the city peaceful for the moment, when the emergency summons had come. She should have known the quiet was too good to last, even with Matt Sheppard sent off with plenty of reading material and John safely drugged and sleeping in the infirmary, ignorant of his father's presence. Could've at least lasted long enough for her to eat, though. Instead, all four of them hurried through corridors that seemed endless, all of them lost in their own grim speculations on the probable situation. Odds were their troublesome guest figured into it somehow. Finally, Atlantis' leader found herself standing near the young gate technician, afraid to ask the question. The sergeant simply acknowledged them with a nod, spinning back to the console.

"This came in several minutes ago."

He hit a button, static crackling so loud Elizabeth winced, then began to detect words among the garbled metallic squawks.

"Matt Sh- am in- water! Re- atta- in ple- rescue! At-"

The broken, barely intelligible transmission abruptly cut off, leaving her shaken. She'd wanted to know if this day could possibly get any worse and it appeared she'd gotten her answer.

"Ma'am, Captain Zhukov and Sergeant Stackhouse are already prepping a Jumper. We had a life sign in the water about one thousand feet off the Southwest pier and... Well, it was moving off rapidly. Just as the transmission cut off, we lost the signal."

"And _Odyssey_ is already gone, operating under radio silence."

Elizabeth summed up the dilemma sourly. A quick nod cut off Lorne's question before he asked, sending the major off to the Jumper bay at a run. With their best pilot, John, injured, Lorne was the most likely to pull this off. She just prayed they weren't too late already, for John's sake if not that ass, Matt Sheppard. She already dreaded having to tell him his father was here, but to then have to inform John that the man died on his first night in the city... Even considering the possibility sent a chill through her body.

"Life sign just reappeared, Dr. Weir. Now 1,236 feet off the pier, moving straight north. Looks like he's caught in the current. Jumper Six just launched."

She let out the breath she'd been holding, relief washing through her. About time they caught a break.

"Why would the life sign disappear like that?"

The Atlantis leader directed the question at the Canadian tech seated in front of her, but the answer came from his fellow countryman behind her.

"If he was pulled deep enough under the water, Atlantis' sensors wouldn't be able to find him. Not without the boost our subcutaneous transmitters provide."

Rodney continued rapidly typing on his tablet PC even as he spoke, unconsciously dominating the room in a way he displayed only in the deepest crisis. Without so much as an 'excuse me', he dislodged the tech from his seat, quickly transferring information until a revised diagram of Atlantis and the surrounding ocean popped up on the screen, a dot showing Matt's position clearly in the middle of the north bound deep ocean current where it surged briefly to the surface.

"Just how does Lorne plan on retrieving him in a Jumper, anyway? He's in the water!"

Elizabeth sighed at the question, reminding herself that just because it had been explained several times in Rodney's presence didn't mean the genius was paying attention.

"Its standard rescue procedure, Rodney. Open the back hatch of the Jumper, send a diver into the water with a harness, then haul them both up using a winch. Jumper Six was modified for just this type of emergency, remember?"

This kind of forethought was exactly what made her second in command so valuable to her. John tended to plan for every foreseeable emergency, then wrack his brain to come up with more. Absolutely no stone would be left unturned in the protection of this city and her people, not while Lieutenant Colonel John Sheppard was around. For all his good-natured, laid back attitude and occasionally juvenile sense of humor, Sheppard took his responsibilities very seriously indeed, a little fact Elizabeth strongly desired to shove in Matt's face at the earliest opportunity.

"_Lorne to Atlantis._"

The call jolted her out of her thoughts, hand quickly coming up to tap her com, praying for good news.

"Go ahead, major."

"_We have our wayward guest, ma'am. Requesting a medical team meet us in the Jumper bay. Looks like hypothermia and a leg wound, maybe a blow to the head as well."_

Injuries to the leg and head? She met Teyla's shocked, concerned gaze with her own. If the iratus had truly been an attack and this was another, a direct one this time... They needed to get a handle on what was going on fast, before this escalated even further. She turned, worried, and headed for the bay herself, Teyla and Rodney silently joining her.

The Ancient craft was already gently setting down, though missing some subtle finesse she couldn't quite put her finger on that was only there when John was at the controls. Nearby, medics stood at the ready, a frowning Carson Beckett in the lead. Like the man or not, the doctor would give the colonel the best care humanly possible as long as he was a patient, but he didn't have to be happy about it. After finally prying what their unwelcome guest had said out of Bethany earlier, Elizabeth could fully understand the cold attitude of the medical staff. As soon as the Jumper hatch opened, though, Carson led the way in. The others stayed outside, certain the team would reappear momentarily with their patient.

Except they didn't. Several minutes passed silently, none of them quite ready to risk Carson's wrath by popping a head inside. Denied the target he truly wished to take a piece out of by his own professionalism, they wouldn't put it past the Scot to go off at the first convenient alternate to show up. Finally, the doctor himself saved them the trouble by coming out alone, waving them over.

"Stubborn fool is insistin' on speaking with the three of you and Major Lorne before he'll let us move him." The Scot's disgust with the elder Sheppard was clear. "Make it as quick as you can, I need to treat him."

A snort from Rodney answered the doctor's annoyed request. Elizabeth felt her own lips twitching in response, caught momentary mirth dancing in Teyla's dark eyes. Seemed father and son were more alike then they'd thought. Carson's exasperation was always a good sign, however, since it usually indicated that whatever injuries there were weren't that severe. Had they been, he'd have already had the man in the infirmary, protesting all the way if necessary.

Knowing it couldn't be put off any longer, they accompanied Carson back into the Jumper, skirting the waiting gurney. The elder Sheppard was seated on one of the forward passenger seats, wrapped in several blankets but still visibly shivering. One leg was stretched out in front of him, where a medic knelt, carefully cleaning several cuts. Lorne, still seated in the pilot's chair, was soberly watching the proceedings.

"Mister Sheppard, I understand you've insisted on seeing us?"

Elizabeth's slight emphasis on the civilian title had the man wincing, one hand going automatically toward a dark bruise forming on his forehead until Carson grabbed it, smoothly taking the medic's place.

"You don't want to be touchin' that anytime soon."

Matt nodded at the advice, then promptly flinched again at the throbbing the move stirred up. Instead, he flapped a hand dismissively, exhausted.

"Look, just- Call me Matt, it'll make things a lot easier on all of us. I haven't been 'Mister' Sheppard since I was twenty-one."

The diplomat was too shocked to say anything for the moment. This was the most reasonable, friendliest thing she'd heard from the man, leaving her wondering if there were some undiscovered magical element to Atlantis' sea water! Then she took a long, hard look at him, studying his posture and thinking over not just what he'd said, but _how _he'd said it. The words had been ever so slightly slurred, easy to pick up with her ear for speech and languages, and his eyes weren't quite focusing on her. Concussion. The signs were all too familiar to her from the many times John or another member of his team had returned with similar symptoms. A quick glance down at her crouched chief medical officer confirmed it when he gave her a short, sharp nod. Silence stretched for a long moment as the others waited for the former colonel to begin while he stared around himself at the Jumper, suddenly fascinated.

"Were you attacked?"

Teyla's soft verbal prod snapped the injured man's attention back to the small group gathered around him.

"What? Oh, yeah... Attacked, yes, out on one of the balconies near the infirmary."

Matt closed his eyes in concentration, stress lines standing out on his face as his expression tightened. Beside her, Elizabeth felt Rodney begin to stir impatiently and quickly clamped a warning hand down on the scientist's arm. This was their best chance for a description and they really didn't need the abrasive Canadian distracting the other man with needling. Finally, Matt sighed, relaxing and opening his eyes in defeat.

"I'm sorry, I just didn't get a good look at him. It _was _a man, dark clothing, came at me out of the shadows." He reached for his head again, Carson firmly intercepting it. "We went over the rail together, must have been when I hit my head. Don't remember doing that..."

Matt trailed off, a little dazed, the concussion obviously causing problems with his concentration.

"What happened to your attacker after you hit the water, sir?"

Lorne was sitting rigidly, almost at attention, his jaw clenched in anger, though Elizabeth wasn't quite sure who the soldier was mad _at._

"He vanished after we hit the water. Listen, can you send someone to retrieve my things on the balcony? There's a letter that I'd rather no one else read, its personal."

"I'll see to it."

Elizabeth reassured the man absently, focused on what had been said about the attacker. None of them thought that they could get so lucky that the man had simply drowned.

"Then what the hell happened to your leg?"

Rodney snapped at the injured officer, almost accusatory. Matt, however, just wearily shrugged.

"Some weird alien sea monster grabbed me until I planted my other boot in its face. You tell me what's around that could do that, you're the ones who live here!"

A sea creature. Only a Sheppard! Feeling her own head begin to throb, she caught Major Lorne's eye and gave him a nod, which instantly had the soldier reaching for his com.

"All military personnel, third down. Repeat, this is Major Lorne, third down."

Teyla nodded in approval even as Rodney gave a disgusted snort.

"Third down?! Sheppard really needs to come up with some more creative codes. I mean, really, American football? And isn't locking down the entire city a little drastic, Elizabeth?"

"No, at least not until everyone is accounted for. It may be our best chance of finding the attacker, who probably knows something about the iratus bug, as well. Two incidents in less then twelve hours seems a bit much to be a coincidence, wouldn't you say, Rodney?"

The words had come out harsh, biting, and she silently berated herself for losing her temper with the astrophysicist. He was worried and hence, tended not to think before he spoke, she knew that! Some might judge the command as over the line, too, even herself three years ago, but not anymore. For most of Atlantis, it would be a few idle late evening hours stuck where they were and some nosy questions. Irritating, annoying, but not exactly harmful. Besides, this time she could actually _do _something about what was happening instead of uselessly waiting for information that might not come from someone who might not truly be an ally... And even when the information came-

"Elizabeth? Dr. Beckett wishes to move his patient from the Jumper."

Teyla's hand on her arm, giving it a gentle shake. A glance around confirmed the Athosian's words, Sheppard wrapped in more blankets aboard the stretcher just in front of her. She could have sworn it was empty just a second ago. She'd become so lost in her thoughts that she'd completely zoned out her surroundings. Again. Hastily, she moved out of the craft, not even bothering to argue with Carson's muttered order to get some rest herself. With two Sheppards in Atlantis, she was sure to be needing it tomorrow!

TBC...


	9. Ch 8: A Time for Pain

Disclaimer: Stargate: Atlantis and all characters therein are the property of MGM. This story is for entertainment only and the author is in no way profiting from it, nor exercising any claims to Stargate Atlantis.

Title: A Time to Heal

Author: Pyrodragon2006

A/N: Thank you so much to all who review, as it really motivates me!! By the way, I was asked, so I'll tell you I think that this story is going to come out around 15 chapters long. Thanks for sticking with me! Now, on to John...

Chapter 8: A Time for Pain

Pain. That was the first sensation John became aware of as he fought his way up through the haze of drugs. It completely enveloped him, a worn blanket, full of blessedly pain free holes in a few areas while so thick in others he squirmed, desperate to find a way to kick it off. Arm, hand, throat, head, ribs... It was one particular spot, though, that focused his attention, forcing him to frantically resist the urge to vomit. Panic left an acid taste in his mouth, heart beating wildly in his ears. His left arm _burned, _pain spiking, stealing away thought of anything else, just as it had so long ago in his neck. John had once believed nothing else could ever hurt so badly. He'd been wrong. The slow drain of an iratus bug was agony, but Kolya's captive- words utterly failed to come close. The only thing that had kept him going was the certainty that his family would come for him, and they had. Hadn't they? So why was he feeling it now? And why didn't they get it OFF?! A cold, dreadful chill washed through him as the pain refused to subside into the horrific memory it was supposed to be.

Shaking so hard his teeth rattled, John surged upright even as hands grabbed at his body, voices shouted, called to him. Eyes locked on his left arm, he saw it there, big, ugly, soft body pulsating as it fed.

"No..."

He moaned the word hoarsely even as he raised the heavy limb and its ugly passenger, intent on beating it against the bed railing, heedless of the agony the move was sure to cause. Or he tried, at any rate. After the first hit, which brought tears to his eyes, the colonel's arm was grabbed, trapped by an iron grip he was too weak to break. Wraith! Only a Wraith could be that strong! Wide hazel eyes flicked up to see the green face, mouth stretched in a sickening approximation of a smile, eyes gleaming in sadistic anticipation of a meal. The hand not holding his arm came back, poised to plunge to his chest-

"No! No! No more! Get out, remember? Have to get away! Kolya! NO!"

Except instead of hitting his chest, the other hand grabbed his right shoulder, giving him a gentle shake.

"Sheppard! You're dreaming!"

His vision grayed out and he slumped limply back against the pillows even as the pain in his left arm began to ease. Suddenly aware that he was gasping for breath after breath though some sort of mask pressed into his face, he tried to turn away, but more hands stopped him. Instead, he concentrated on consciously controlling his breathing, his vision clearing as well. He found himself locking gazes with a grim Ronon. Vaguely, he began to discern the tell-tale beeping of a heart monitor and the soothing burr of Carson's voice through the white noise in his head.

"That's it, colonel, just relax and let the pain medication do its job. Just dream combined with the last of the anesthesia, that's all. You're safe on Atlantis..."

Turning his head to the left, he met the doctor's concerned gaze, relief washing away the last remnants of the hallucination. A dream. Just another in his parade of Friday the 13th nights lately, though the inclusion of that damned bug was new. Seemed his mind was inventing new nightmares to torment him with now. Must have been a doozy to land him in the infirmary. He swallowed convulsively against the taste of acidic bile in an otherwise bone dry mouth, grateful when Ronon and Carson carefully sat him up a little to sip on some water. Settled back down, John turned his face from his friends in embarrassment, berating himself for being so weak and half afraid to ask how much damage he'd done to himself. Memory whispered in his mind, so real he could swear he heard the cold, harsh voice.

_"Military officers can't afford to be close to those under them. Personal stories and sharing a laugh can get you all killed, distract and cloud your judgment. You're a soldier in a war zone, and the Air Force doesn't want you to be human!"_

_The door to his room slamming shut echoed in his head, leaving the quaking, sobbing six-year-old John in a miserable ball on his bed._

"Colonel? Son, I need you to look at me."

A gentle hand on his shoulder brought him jolting back from the past to find the physician worriedly watching him. Not that _that _was anything new. Worried seemed to be Carson's perpetual state around him recently. Gingerly swallowing around the harsh bump in his throat left by an intubation tube, he met the doctor's eyes.

"Sorry, doc, guess I zoned out for a minute."

Carson's expression took on a hint of sympathy as he nodded reassuringly. Between lack of solid sleep and the trauma he'd suffered, John's concentration lately was often fragmentary at best. Hence the files he'd left sitting on his desk...

"The meeting! I was supposed to be there! What the hell happened?"

Ronon's large hands hovered, ready to restrain him again as more recent memories cut through the fog in the colonel's head. John, however, had finally forced himself to full lucidity, and knew better than to try moving at the moment. His left arm still throbbed, albeit muffled by the drugs, as Carson set about carefully checking it. The last thing he needed was to do something stupid and make things worse! As the doctor slowly unwrapped blood-spotted gauze from his hand to just above the elbow, revealing four long, stitched wounds, the pilot swallowed hard. At least he hadn't torn open any of them.

"What happened, doc?"

He asked again, his voice a hoarse whisper. Somehow he doubted he'd like the answer, especially when Carson silently redressed the wounds before meeting his eyes again.

"Do you remember actually getting to your office for those files, John?"

O-kay, Carson addressing him by first name meant they'd moved from worrisome to downright alarming. Now the doc was running through his vitals, including taking his pulse in _both_ wrists. Doing his best to ignore the familiar routine, John searched his memory, realizing with a frown that it stopped dead at the door to his office with only a deep sense of dread beyond. Mutely, he shook his head. Carson smiled sadly.

"Aye, that's not unexpected, son, not with the severity of the phobic reaction you suffered. Your mind is protecting itself."

His stomach plummeted further, if that were possible.

"Phobic? Protecting itself against _what_?"

This beating around the bush was beginning to get more than a bit irritating!

"Somebody left one of those bugs on your desk."

Ronon's impatient rumble interrupted Carson before he could come up with another delay. Even as the officer reeled in horror, he was grateful for the Satedan's blunt, no fuss style, tired of being coddled. It didn't stop his body from beginning a mindless shaking, though, nor prevent fear, insistent, immediate, from coursing through him. His gaze flicked around the room, searching for that haunting black shape even as the rational part of his mind told him he was being ridiculous. There was no way his friends would be calmly standing there were there the slightest chance of an iratus bug being in the room.

"I shot it. Its dead, Sheppard."

Yeah, the Satedan probably blew it into tiny pieces. He was quite pleased with that calm, reasonable conclusion, firmly overruling the irrational panic. Soldiers couldn't allow fear, either, especially leaders.

"Buck up, John, you're being an idiot!"

"You're certainly not an idiot, colonel! The apprehension is a perfectly natural response to everything that's happened!"

Carson's stern admonishment took him by surprise until he realized he must have spoken his last thoughts aloud. Time to quit freaking out and start being Atlantis' military commander.

"What's the situation, Carson? What's wrong with my arm?"

The doctor began studying the digital thermometer he was turning over and over in his hands, a sure sign of one very unhappy Scot. Never a good thing for John.

"Carson?"

He prodded again, barely over a whisper.

"The iratus leaped at Elizabeth and you pushed her aside, colonel. It latched onto your arm, tore open an artery before you flung it down the hall an' Ronon killed the bloody thing. You should heal just fine, but right now you need to try getting some more sleep, its about midnight."

Panic bubbled just under the surface, waiting to erupt again.

"Those-" His voice broke, and he cleared his throat nervously. "Those things aren't known for letting go of a meal."

A sober, deeply troubled look.

"Aye, colonel, I know, but I don't want you worrin' about it." John was tempted to tell Carson just how dumb telling someone not to worry about something that obviously _was _a gut-wrencher really was. "I'll run some tests and Major Lorne, Teyla, and Rodney are already workin' on how the bloody critter got in the city. Even our unwelcome guest is sleepin' off his involuntary evening swim, so-"

"Wait a minute! _What _unwelcome guest? I don't remember _Daedalus_ arriving."

No doubt Caldwell was waiting to spring on him come morning with a laundry list of what John had done wrong now. The man never failed to throw anything he could in the younger officer's face. Irritably, he scrubbed his good hand over his face, careful not to dislodge the IV.

"I'm sorry, son, I forgot you wouldn't have heard. _Daedalus_ was attacked just after she left Earth. Minor damage, from what I understand, but enough for the _Odyssey_ to come instead. They've already off-loaded and gone." Carson hesitated a long moment, as if deciding what to say, which instantly made John uneasy. What could have happened now? "This presidential adviser of yours has managed to make himself a right unpopular bugger already and was tossed from a balcony about four hours ago. Wound up a bit cold, but no real damage done."

John smiled slightly at his friend's sour summary, hearing the accompanying snort from Ronon. At a guess, 'unpopular' was an understatement! No matter, that could wait.

"There's a letter for you that was brought in, too. Its on the bedside table when you want it."

A letter? Shock rolled through him at that one. In all the time John had been on Atlantis, the only mail he'd received had been official communications from the military and his magazines. From Carson's frown and too casual tone, this couldn't be anything so routine. Sleep was pulling him down, but curiosity won for the moment.

"Whose it from?"

"I don't know, colonel, it just has your name on the front and one-six-zero-zero P. Avenue in the corner."

He just lay there letting that one sink in, a bit surprised that Carson didn't recognize the address, then he kicked himself. Why should he, Carson was Scottish!

1600 Pennsylvania Avenue. The White House. Henry Hayes. Crap.

There could be a thousand reasons for such a missive from his father's old friend and he was sure he wouldn't care for a single one of them. He settled for a weary sigh and closing his eyes, feigning sleep. Whatever it was could wait for the morning, he was hurting too much to deal with the jumble of emotions the message was certain to evoke. He'd never taken advantage of his family's well known connection with the rising political star, hadn't seen the man in over ten years, but it had marked him nonetheless. Certainly kept the brass tip-toeing around him after Afghanistan and probably contributed to John only receiving a black mark on his record instead of a court martial and dishonorable discharge, though. Which, of course, was what his irate CO had recommended.

Mind still going in circles over his past, John allowed the relentless exhaustion to pull him back down, hoping to achieve a few hours of normal sleep before the next inevitable round of nightmares set in.

It was early the next morning when John came awake to raised voices with a start. For a while, he just lay there, images and memories flitting through his drug-fogged mind, important but too elusive to truly grasp. He knew he'd slept longer than he had in days, but it hadn't been at all regenerating, nightmares and drugs not typically his choice for a restful night. Had he dreamed the damned bug after all? No, he distinctly remembered Ronon telling him he'd killed the thing and why else would he be back in the infirmary just days after being released? Well, he'd wanted everyone to quit treating him with kid gloves over the Wraith, he should have been more careful what he wished for!

John laughed softly at himself as he opened his eyes, taking in the familiar sights of the small medical isolation room. Sure enough, his large team mate leaned against the wall by the door, apparently scowling at whatever was occurring outside. The colonel gingerly hiked himself up into a semi-recline on the bed, mindful of his injured arm, and cocked his head, working to identify voices over the beeps of nearby machines. The first was easy, Bethany Kirran telling someone off with language he wouldn't have dreamed of the petite lady using. The second, a male voice that rose in answer, though... John felt his blood run cold.

"Tell me that's not who I think it is."

His hoarse, apprehensive whisper brought the Satedan around to face him even as the argument in the outer infirmary abruptly cut off. The anger and hint of sympathy in the face of the normally impassive man told the Atlantis CO everything he needed to know.

"Shit."

He slumped back, weary beyond words, wondering what deity he'd offended to have the new life he'd built begin to unravel this way. Why?! Surely the president of all people knew how Matt Sheppard felt about his son, why deliberately throw them together?! His restless gaze settled on the plain white envelope laying on the table nearby. With a sigh, he grabbed it and tore it open with his teeth, heedless of the danger of tearing the letter inside. He just wanted it over with. A single, hand written page dropped out.

_Colonel Sheppard,_

_I realize that as one of your father's oldest friends, I may not be the most popular person with you right now, but as the man a young boy was called 'uncle', I'm asking that you at least consider my words._

_From all accounts, you've been doing a pretty incredible job out there, so I've tricked your father into going to Atlantis in the hopes that it can open his eyes to a few things. There was an awful lot of pain, anger, and guilt four years ago- on both sides- but they say that distance can bring perspective if not healing. You both need to face this, John- before all that is left are regrets. _

_At the very least, try not to kill each other. I need you both and don't have time for all the paperwork!_

_No matter how this turns out with Matt, know that you continue to enjoy the confidence and respect of myself and Generals O'Neill and Landry. Damn fine job, son._

_Respectfully,_

_Henry Hayes_

Talk about hitting a man when he was already down! Crumpling the letter one-handed, he flung it as hard as he could at the far wall, ignoring the sting of his IV pulling from his hand. The president was right about time bringing perspective, but instead of healing had come regret and a bit of anger. Somehow he doubted the great Colonel Sheppard had mellowed even that much, but...

Determination set in as he carefully sat up, swinging legs over the edge of the bed as he silenced the monitors, then began pulling leads. Ronon didn't look pleased, but thankfully didn't try to stop the pilot, either.

"What are you doing, Sheppard? Doc said you weren't supposed to be up."

"I need to see Elizabeth, then _him_. I'm not sitting around anymore, Ronon. Tag along or get the hell out of my way."

The Satedan paused for barely a second before making his decision, offering his team leader a steadying hand. Unfortunately for John's stubborn streak, he needed the help, too, or he would have landed in an undignified heap on the infirmary floor. Ronon reached one long arm around him to the table and snagged a pair of slippers for the injured man, dropping them to the floor so John could simply slip his feet into them. The colonel did so, then gritted his teeth and silently accepted Ronon's help in slowly making his way unnoticed out the back door of the infirmary. Right now, his single-minded concentration on reaching his goal had him willing to accept almost anything. Too bad his body didn't agree, forcing them to a turtles' pace and frequent stops for rest. It seemed to take forever to reach Elizabeth's office, which left John's mind plenty of time to run through 101 versions of the coming confrontation, over and over, none of the outcomes good. What he heard uttered in that cold voice as he reached the door to the diplomat's office, though, was beyond what he'd feared.

"My son? I don't have one anymore. My son died in Afghanistan."

Not that much earlier...

Morning found Rodney, Teyla, Carson, Major Lorne, and Elizabeth all gathered in the latter's office to report on the various aspects of the investigation. None of them had managed much sleep last night, worried about John and recent events, not to mention jumping at bug shaped shadows, though none was likely to admit it. The city was no longer on lock down, but everyone was being restricted to the secured perimeter for now and off-world travel was still suspended.

"Carson, why don't you start? How are your patients this morning?"

Elizabeth turned to her CMO, all of them anxious to hear the answer, though it certainly wasn't the elder Sheppard's condition they wanted to know. Carson, however, had his own priorities, pulling a distasteful grimace at the thought of his more irritating patient.

"Matt Sheppard will be released this morning to rest in his quarters if Bethany doesn't strangle him first. The two of them react like a spark in a flour mill, instant explosion. All the scans were clear, his body temperature normal, and the bite on his leg wasn't severe. He'll just be limpin' a bit."

Rodney snorted in amusement. "Sounds like even the sea life has good taste. Found Matt Sheppard unappetizing, no real surprise there."

That brought brief smiles around the office, lightening the mood a bit. They'd long known there were large creatures in the ocean around Atlantis, just hadn't had an opportunity to do any extensive studies. At least Elizabeth didn't have to figure out how to explain to the president that his newest adviser had been eaten.

"Can't blame the thing. Talk about biting into something bitter!"

Lorne added, earning a few laughs.

"And John?"

She prompted Carson, noting how quickly the others sobered. The Scot saw it too, nodding.

"Aye, that's a horse of a different color, isn't it? Once the sedation wore off, he went back into that bloody cycle of nightmares he's had for the last week, including hallucinations at one point, partially due to the medication. Ronon being with him seems to help a mite, but his body and mind aren't getting any true rest, which is what he needs to heal. I've put the colonel on a low dose of Lorazpam, but we need to figure out how to break the cycle. He's also havin' symptoms of a severe phobic reaction, which isn't helpin' matters any, though I expected it."

"What? Colonel Indestructible, afraid of something? You're joking, right?"

Rodney looked to his team mate for support in his breezy dismissal, only to find Teyla staring at him in surprise. Elizabeth, Carson, and the major were all pinning him with looks clearly shouting 'idiot'!

"What?!"

"Rodney, he's been showin' signs of entomophobia since his first encounter with the critters! The way the colonel avoids mention of the bloody things, the nervousness when they _are _brought up, his strict refusal to allow even a dead specimen brought back to Atlantis? Those are all classic symptoms! One of the mind's ways of dealing with that level of trauma is to ensure no chance of a repeat encounter. Its not very healthy or always rational, but it _does _happen. The real question is what daft bugger provoked it and why."

"I'd like to hear the answer to that as well. That is, if I may sit in?"

The new voice called their attention to the door where a somewhat pale Matt Sheppard stood. He was dressed in the standard Atlantis uniform with the black panels signifying military, the resemblance to John so strong it took Elizabeth's breath away. The last time she had seen her military commander on Kolya's grainy transmission, he had looked very much as his father did now, albeit not as healthy. With a shudder, she firmly shoved the disturbing image from her mind, a glance around the office meeting grimaces and reluctant nods. No one really wanted the elder Sheppard around, but like it or not, the attack last night made him a part of this whole mess.

"Please..." She paused, deciding how to address this walking font of trouble. "Matt, come in. How are you feeling?"

"I'm good, thank you, Dr. Weir. Were you able to locate my attacker?"

Atlantis' leader differed that one to Major Lorne, who didn't look happy.

"Unfortunately, no, sir. Even with the immediate lock down, everyone was accounted for and either bone dry or just out of a shower. No real evidence was found at the scene, either, though no one here is trained for that. Recovered your letter, but the computer was gone."

Matt frowned, green eyes sparkling in anger.

"I'm sure your people didn't miss anything, major. If your head count didn't turn up anyone, then..."

He allowed the sentence to trail off, but not in accusation, just inquiry. Elizabeth almost demanded to know what someone had done with the real Matt, this man was so different from the officious jerk they'd had foisted off on them yesterday. It had been a full two minutes and no one seemed to be contemplating gross bodily harm!

"Then we may have an intruder in the city. Wouldn't be the first time we've had someone hide in a shielded area or where the sensors are still down. There was a huge gap where the gate shield wasn't even up during that whole mess with Lucius."

McKay shot the others a pointed look as he spoke. There were winces all around at the mention of that particular mess, especially since John was the one who'd saved them. Again. Now their lapse may have had more dire consequences then they'd thought.

"That does not explain the attack upon Matt Sheppard last night. If they have been successfully hiding for so long, why risk exposure now?"

The colonel stiffened at Teyla's question.

"The computer Dr. McKay gave me! You said there were classified reports on it and it wasn't on the balcony!"

Rodney shook his head. "The shoulder strap was found tangled around the rail, ends torn. Its either smashed on one of the lower levels of the city or on the bottom of the ocean."

Matt sighed. "Alright. So where do things go from here?"

Elizabeth's knuckles began drumming a nervous staccato on her desk. It was a good question, but one she was still debating the answer to. The diplomat was grateful when the others respected her prolonged silence, even Rodney, patiently waiting.

"The investigation will continue as I believe you mentioned a few more leads still to be explored, major. Rodney, I'd like you and Radek to carefully go over the city's sensor logs for the last few days as well as any logs we have for the Jumper trips to iratus planets. I realize its a long shot, but maybe we'll get lucky. Carson, I need to speak with you and Matt for a moment, so don't go anywhere. Everyone else, dismissed."

"Wait a minute, Elizabeth, what about Kolya?"

Everyone froze at the cold hatred in Rodney's tone, the suppressed rage sparkling in his blue eyes. The Atlantis leader winced as she realized these new problems popping up so suddenly had actually made her temporarily forgot about the absolute hell John had just faced.

"There's not much we can do, Rodney. I spoke with Ladon the other day and he'll inform us immediately as to any leads, plus Teyla and Ronon have been alerting their contacts."

Lorne caught her eye as she spoke, a half-nod letting her know he had something to add.

"Major?"

"Thank you, Dr. Weir. Colonel Sheppard and I have already discussed the situation- don't give me those looks, he insisted- but there's only so much we can really do to guard against another ambush. All teams have been given strict capture or kill upon contact instructions, per terrorist protocols. Basically, if there's the slightest risk to themselves or another member of the expedition, they've been given permission to use lethal force and get out of there."

The taut voice, filled with quiet rage, told everyone in the room what Lorne and the rest of the military thought of the situation- if there was the risk of a hangnail, they'd kill the man. There was almost no chance Kolya would be coming out of any further encounters with an Atlantis team alive. Elizabeth bit her lip, but didn't contradict Lorne's interpretation. She'd learned some harsh lessons in the Pegasus Galaxy, changed in ways both good and bad. That she would be capable of calmly ordering the death of another human being- it was inconceivable to her before last week. Yeah, sure, she'd ordered operations, knowing they could involve deaths on both sides, but she'd never before crossed that fine line. Never knowingly sent them to kill, not capture, a fellow human. Before, the situation, the trauma of watching a good friend tortured, had offered some excuse for her actions, but now... One glance at the haunted expressions of Lorne, Teyla, Rodney, even Carson, and she knew she was doing the only thing she could. Maybe. Right or wrong, she'd live with it. No wonder Jack O'Neill had warned her that she'd have gray hairs before long!

"Anything else, Rodney?"

A mute head shake, always a bad sign with the Canadian. She'd have to keep an eye on him, make sure he was dealing with what he'd seen.

"Okay. Dismissed."

Lorne, Teyla, and Rodney filed out, Elizabeth watching them as they conferred briefly before walking off together. It was a blatant delaying tactic on her part, but neither man pushed to open the discussion they all knew was coming. The only one she was dreading more would involve John.

"How much does he know, Carson?"

She finally turned to face them both, deciding silence was getting them nowhere. Her chief medical officer looked as tired as she felt, with deep shadows under his eyes and new worry lines creasing his face. Not surprising. None of them had been able to enjoy a restful night in almost a week, plagued by their own nightmares courtesy of Kolya. With all the people who had seen one or more of the transmissions, Kate Heightmeyer was the most overworked person on Atlantis.

"Not much. I told him about the incident last night, but didn't mention a name. He didn't seem to notice, either, but he was fairly groggy from the medications. He needs to be told soon, though."

The diplomat pursed her lips in displeasure, arms crossing, but nodded, only to be brought up short by Matt Sheppard's snort.

"Tell him what, exactly? As far as I'm concerned, he's Lieutenant Colonel Sheppard, the military commander of Atlantis, and I'm a visiting presidential adviser, nothing else."

Jaws dropped open at that. Wide-eyed, Elizabeth just stared at the older man in disgusted shock even as Carson's face slowly tinged bright red. After the former colonel's asinine remarks yesterday, she hadn't thought anything coming from his mouth could leave her gaping again. She'd been wrong.

"He's-"

"My son? I don't have one anymore. My son died in Afghanistan."

A muffled gasp from the doorway brought them all around to see Lieutenant Colonel John Sheppard standing there, pale, swaying slightly, arm carefully nestled in a sling. For just the briefest instant, Elizabeth saw John's guard go down, the depth of pain in his haunted hazel eyes taking her breath away, then the shutters dropped once again. Deep anger took the place of the emotional agony, as cold as the Arctic wind. Without a word, John turned and slowly walked away, body rigid, each step carefully measured. Ronon, who had been just behind his team leader, scowled at Matt menacingly, then followed his retreating friend.

Tbc...


	10. Ch 9: A Time to Find Peace

Disclaimer: Stargate: Atlantis and all characters therein are the property of MGM. This story is for entertainment only and the author is in no way profiting from it, nor exercising any claims to Stargate Atlantis.

Title: A Time to Heal

Author: Pyrodragon2006

A/N: Wow, you guys are great! Thanks so much for the reviews, you've got me typing like mad to get more up. That includes the next chapter of Fate's, for those reading it. My beta is helping iron out a few problems, but it should be up tomorrow or the day after at the latest!

Chapter 9: A Time to Find Peace

John felt himself gripping the balcony railing so tightly his fingers started to ache, but it kept him from slamming a fist into the wall. He should have known better, really, then to allow himself to hope for even one moment that his father would be willing to change. Once Matt Sheppard made up his mind, that was it, the subject was closed. The man was close-minded in the worst way, as John saw it, an attitude all too prevalent in the military.

Growing up, he and Melissa had both known that Father was the final judge and jury on all things, no appeals allowed even by Mom. Of course, that was only when he was home, which was roughly half the time, even though they moved from base to base with him. Like any kid, John had rebelled, but he seemed to have an innate sense of where the line was between simply irritating his father and provoking full punishment, skirting it but rarely crossing. It was an ability that had come in very handy as an adult with stuffy CO's, including Sumner the brief time they'd served together. Matt had always been tough with his children, especially once John declared he wanted to be a pilot- at age five- but relatively fair. Now, though... a Wraith had been more open to him, more accepting, than his own father.

Horrified, he felt the pinprick of tears attempting to well up and hastily reached to wipe them away. Without the stabilizing death grip on the rail, however, he began to sway precariously, an exhausted body threatening to fold. Gray danced at the edges of his sight while dizziness swept through him and he felt the solid bulk of Ronon move to stand beside him, ready to catch him should he finally give in and collapse. John fought with everything he had left to stay standing and conscious. He wouldn't, _couldn't,_ allow himself to show weakness, not now, not with _him _here. He hadn't shown any to Kolya when faced with a Wraith slowing taking his life, even needling the Genii about his blustering threat to invade Atlantis, so he sure as hell wouldn't be starting when he was back home. This city and her people depended on him to be the strong, indestructible Colonel Sheppard, protector, not a human being suffocating under the weight of traumas past and present. Except this was finally too much. He could feel himself faltering, unsure of what to do or where to turn. His body shook as much from the force of emotional and physical storms raging through it as from the wind cutting through the thin scrub top.

"John? You need to sit down before you collapse."

Elizabeth, gently resting a hand on top of his own, which once again strangled the railing. The soft squeak of wheels announced Carson and a wheelchair arriving on his other side. He'd probably be catching it from the doc for being out of bed, but John was simply too tired to care. It wasn't like he could truly rest when he _was _laying down, anyway- Matt Sheppard, Kolya, the Wraith, the mysterious appearance of the iratus bug, lack of sleep... All of these kept his mind active, though he couldn't force it to focus on one problem for more than a moment before it flitted on to something else.

"One problem at a time, just like always. It doesn't matter what _he _thinks. Come on, John! What the hell's the matter with you?!"

The last part was screamed. At himself, his uncooperative mind, the Pegasus Galaxy, fate, his father, he didn't know. He felt more than saw Elizabeth flinch away from his cold rage, as she had after he so calmly shot Kolya past her head. She must think he was a stark raving lunatic by now. Sure as hell was acting like one.

"Sorry. I just- Sorry."

The apology was mumbled as he closed his eyes, head bowed, unable to look at them. He'd never allowed himself to lose control around them before, not like that, when he teetered on the very edge.

"Its alright, John, that's trauma and exhaustion talking. Right now, though, you need to let Carson take care of you. Don't worry about the bug, our presidential adviser, any of it, I'll handle it. Your only job is the health and well-being of John Sheppard."

Well, one of the aforementioned problems he had every intention of ignoring anyway. It would be easier not to try relating to the man as any kind of parent, he decided, since he sucked at the whole emotional thing anyway. John had just been caught flat-footed by his fa- Matt Sheppard's pronouncement, with emotions he hadn't even known were there leaping uncontrolled to the surface. There was one situation tying his guts into knots that couldn't be placed on the back burner, though.

"He's still out there, Elizabeth. What if next time its Rodney or Carson or Teyla? Or _you_?"

A glance from the corner of his eye told him he'd caught her completely by surprise with that one, though she didn't ask who he was referring to. On his other side, Carson was sputtering, eyes wide, though whether it was because of the rapid subject change or the prospect of being subjected to the same kind of torture John had just gone through was hard to say.

"Kolya will be dealt with, John. I told you not to worry about it for now, that's an order."

John sighed heavily at that, but uncharacteristically didn't feel up to fighting her on it. Which should have set off warning bells by itself. Instead, he slowly lowered himself into the wheelchair without further prompting. She was right, with gate travel suspended at the moment, there _wasn't _anything he could do. Now, if he could just stop looking over his shoulder for that stupid torpedo weapon... get Kolya's smug voice out of his ears... quit the phantom pains in his chest he'd 'forgotten' to tell Carson about... and now stop seeing bugs around every corner...

Head resting on his good hand, he didn't object when the wheelchair was gently swung around. Instead of heading to the infirmary, however, the doctor stopped with John now facing the interior of Atlantis and took a seat on the bench across from him. Out came the basic medical instruments Carson never seemed to be without, which finally drew another reaction from the silent colonel, albeit only a wisp of a smile. He sat patiently through the exam, ignoring the increasingly alarmed looks Carson and Elizabeth exchanged, mostly because he only caught glimpses of them. He was too busy trying to force his mind to settle on one problem, 'worry it straight' his mom used to call it, but things skittered across the surface of his mind like partially melted ice cubes, too slick to grasp. It was several minutes before he noticed the doctor had finished, settling blankets around John as he did so, and now sat quietly watching him. A brief smile flashed across the Scot's face as John finally made eye contact, the type the doc gave when he had bad news and didn't quite know how to tell the patient.

John sighed. "Carson?"

"Where would you feel the most comfortable, colonel? The one place your instincts tell you you're always safe?"

The pilot just blinked dazedly at the other man for a second, not expecting that one. It also wasn't exactly easy to answer. The other two seemed in no hurry to push him, just waiting. A few years ago, he would have said flying was where he felt the safest, without hesitation, in spite of how often it meant he was getting shot at. There was just something about being up above, with the birds and the clouds, that made him feel untouchable. Now, though...

A slight shiver of astonishment raced through him as his muddled subconscious decided to supply an answer.

"With my team."

Ronon, a silent guardian leaning against the wall through all this, gave a short nod as if his leader's words simply confirmed what he already knew. Then, as military himself, the Satedan would have understanding of how deeply the impact went when a soldier found a team he could truly trust. As John had told the Wraith, they'd come, no matter what they had to do or how long it took. There'd been none of the doubt that had plagued him deep down in his soul as he sat waiting in the Sanctuary last year, not this time. They didn't leave anyone behind because they were family, it was as simple as that. A smile from Carson, a gentle hand resting on his shoulder.

"Aye, I think we can handle that. The infirmary or your room?"

His foggy head couldn't make sense of that one.

"What?"

"Where do ya think you'd be more comfortable having your team with you, John, your quarters or the infirmary?"

Oh. He was really out of it to have missed that one. Carson was using the patient 'I'm talking to someone only firing on one thruster' voice, too. The kind used with indecisive four-year-olds and Rodney in post-crisis daft mode.

"My quarters?" Half answer, half hopeful plea.

Another smile. "All right, son, your room it is. Elizabeth, love, would you mind trackin' down Rodney and Teyla while Ronon and I get the colonel settled? I already asked Bethany to bring an IV and portable heart monitor to his quarters."

John scrambled to process what was going on. Hadn't the day just begun? His team must have other things to do than sit around because he jumped at nothing! Certainly Rodney did!

"What? The investigation-"

His half hearted protest was cut off by shaking heads.

"There's nothing at the moment that can't be handled by Lorne or Zelenka. We don't exactly have a lot of leads right now and your health is more important, John. Besides, Rodney can review sensor data on the computer in your quarters as easily as he can in his lab. No arguments!"

Elizabeth's sharp command cut him off before he could even think one through. It was too much work when they would ignore him, doing what they wanted, and he was just exhausted enough to let them. A weary nod and Carson immediately wheeled him off the balcony, setting a brisk pace through the halls. John was forced to close his eyes as the movement, doors, posts, people flashing by him, began kicking up a queasy stomach.

He must have blacked out for several minutes because the next thing he knew, he was being gently put onto his bed. The slippers he'd donned earlier to make his escape from the infirmary earlier were tugged off and several blankets spread over him. A prick on his good arm told him an IV catheter was being skillfully inserted even as someone on his other side carefully cleaned and re bandaged his wounds. As exhausted as he was, the touch of hands was enough to keep him tense and awake, his subconscious screaming 'danger'. Stupid, really, considering the whole thing was over, had been for a week. No doubt this was making a spectacular showing for a certain retired colonel, as if he didn't have a low enough opinion of the younger man already. After all, it was his fault that-

Stomach acid burned in his throat at the image swimming through his mind, cold, harsh. He couldn't contain it this time, choking as he found himself unable to sit up. Hands rolled him, supporting as what little he'd eaten came back up.

"Easy, John, we've got you." He was eased back down. "Bethany, double check all the test results from last night, please, and rerun the scans. If there are complications starting, I want to know about it sooner rather than later. The colonel's been through enough."

"Will do, Carson. Are you staying here with his team to monitor?"

"Aye, I think I'd better. And if our guest needs anything, it might be best to call Biro to treat him. I don't need any bloody brawls in my infirmary!"

A snort from John's left.

"That could be entertaining. Her bedside manner's worse than Dr. Weir's! I'll let you know if I find anything in those tests."

The soft swish of an opening door.

"About time, Rodney."

"What?! I'll have you know I'm very busy! I need that computer, Teyla."

"Of course, Rodney. I was simply reviewing the latest findings of our investigation. It is-"

At that point, John quit concentrating on what they were saying, content to lay there and let the voices of his team, his true family, wash over him. They weren't trying to be silent, tip-toe around him in the oppressive silence he dreaded. No, this was _normal_. For once, it didn't take long for him to drift into a deep, restful sleep.

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Elizabeth was not a happy woman at the moment and didn't care who knew it. The sensor logs had been a long shot at best because they would only record the locations of life signs with no way to tell who they were. Matched with statements, however, they might have told them if someone was lying. Except they didn't.

When Radek pulled up the relevant time periods from the archives, everything matched. Not only that, but Matt's life sign could clearly be seen going over the balcony rail- alone. No one else seemed to be present. As for John's office, no one went near it until the time of the incident. It shouldn't have been possible.

With a heavy sigh covering the impolite words she wanted to say, she turned to face the equally grim Radek Zelenka and Major Lorne standing next to her. They'd all thought- briefly- that they were finally getting somewhere.

"I thought someone concealing themselves from the sensors was impossible?"

"Outside of certain shielded areas, yes."

Radek's level of frustration was clear from the thickening accent and staccato delivery, reminding the Atlantis leader that it wasn't just John's team who was being deeply affected by all this. Colonel Sheppard was a popular, respected member of the expedition.

"It should be. This doesn't make sense, Elizabeth. Did Radek double check everything with a systems diagnostic?"

Rodney's question over the com had the Czech engineer rolling his eyes, free to show what he thought of the Canadian's straw grasping. The astrophysicist was still in Sheppard's quarters with the rest of his team, keeping watch over the colonel. Who'd been sleeping peacefully for just over four hours now, so long as his team maintained a low amount of noise to reassure him on some level that they were there. The current plan was for them to stay there as long as John needed, even if it meant bringing in cots tonight. At last report, Carson was kicking himself for not thinking of it sooner since a component of the trauma John had suffered was isolation.

"Of _course_ I did, Rodney. Nothing is wrong with the sensors! But for every technology, there is way to counter if one is clever enough, yes?"

"True." A thoughtful pause. "But _I've_ never found a way around them, so how could anyone else?"

Elizabeth had to smile at hearing the typical Rodney arrogance so loud and clear for the first time in almost a week. The scientist's reaction to his friend's torture, not to mention their own failure to find John, had been to shut down, certain the colonel was dead. Once John was rescued, Rodney's entire focus had become his friend and what he went through to the point where Carson had to threaten the Canadian with sedation if he didn't settle down and get some rest. Not to mention quit bugging the medical staff trying to get into the colonel's room. _This _reaction was much more normal.

"You haven't needed to fool the sensors, Rodney. They say necessity is the mother of invention, after all."

Zelenka gave her an assenting nod, along with a look of rather pained resignation. They both knew now that _Rodney_ knew it could be done, he was unlikely to allow the Science Department any rest until he discovered _how._

"Fine. I do now. Radek, have Polanski and... and... the American with the lisp, the new one who never listens to me-"

Surprisingly, it was Lorne who came up with the name first.

"Alex Kennedy? She's deaf, McKay! If you bother to face her when you speak, she reads lips."

"Really? Why didn't anyone tell me that? Never mind, just get the two of them working on it while I start from here. Maybe somebody hacked into Atlantis' main database and altered the sensor logs. What about the physical search the military was doing?"

"We're working on it, doctor, but you know how large this city really is and you just more than doubled our search area. If they don't have to stick to the shielded or damaged areas, we may simply not have enough people to cover everything, especially since you're implying the LSD's won't help, either."

"Well, then, you'd better get your grunts moving, hadn't you? McKay out."

If looks could kill, Lorne would have slain McKay right about then.

"A bit rude, isn't he?"

Matt Sheppard's question had the Atlantis leader startling as she turned. The man had come up so quietly none of them heard him. She allowed a carefully sculpted diplomatic mask to slip into place before meeting his eyes. The Matt who had been quietly moving through the Control Room the last few hours was once again the curious, polite stranger who'd been in her office this morning. He was asking astute questions about Atlantis, off-world operations, and the current situation in the Pegasus Galaxy, not reacting in any way to mention of Atlantis' military commander. It was proving to be a bit disturbing for those who'd heard who Matt really was, especially when one officer told Elizabeth that man had denied being any relation to John. If Kate weren't already so busy... Well, at least the man wasn't causing more problems at the moment, though his ability to change demeanor was spooky, to say the least. Though, come to think of it, she'd witnessed John pull the same trick a time or two.

"The social graces occasionally escape Dr. McKay. When one is a genius, the rest of us mere mortals have to be more forgiving, especially given the number of times he's saved the city."

"Not that he needs reminding of that fact. Sir."

Lorne rolled his eyes in good-natured exasperation, then he and Zelenka headed off, leaving her with their guest. Matt gave the young major a nod, tactfully ignoring the slight pause before the 'sir', she noted. Just maybe he'd gotten the fact that most of the intra personal repair work needed with the Atlantis command staff was necessary on his end, not theirs.

"Quite an operation you have here, Dr. Weir. I'm especially impressed with how well you seem to have balanced the military and scientific sides of the expedition. From my experience, those two groups are usually like oil and water, completely incompatible."

Her mind reeling over what, exactly, she should say, she gestured for the retired colonel to walk with her, headed for the command balcony. Should she answer honestly and risk an explosion or diplomatically smooth it over? Making a permanent enemy of a man who had the ear of the president could prove disastrous, but the way he'd treated John...

"The majority of the credit for that belongs to Colonel Sheppard. He has forged a remarkable ability to work together with Dr. McKay and made sure those under his command followed his lead. Most problems between the two departments are promptly handled before they ever reach me with fairness to both sides. Without John, I honestly don't know how well I'd be able to run this city."

Elizabeth had cautiously timed the end of her statement to coincide with their arrival out on the balcony so any arguments wouldn't entertain the Control Room staff. To her utter shock, though, the man simply nodded, accepting what she said at face value.

"The lieutenant colonel is known within the service for being a maverick, though, not exactly known for his ability to follow orders and obey the chain of command. He can't be an easy person to have as your second-in-command. I've read at least one report where he directly challenged your authority in a way that should have gotten him court martialled."

There it was, full of veiled contempt. Somehow she knew he wouldn't be able to let such glowing compliments go by without taking a shot at John. Now he was watching, gaging her reaction, and she hadn't missed his refusal to call John by name.

"There was at least one incident early on, yes, but the two of us have long since dealt with it, and I'm not military. When problems come up, there is _no one_ I'd rather have by my side. Whatever happened between you two in the past, you obviously have no idea who John is now, nor do you want to. That man has just literally been through hell for this city and I won't tolerate you causing him more problems! Either treat him with the respect due his position here or stay away from him. Also, I trust you won't be allowing that ill feeling to color any report you make to the president or I will personally come to Earth for a discussion you _will not_ care for. Do we understand one another?"

Green eyes snapped angrily at her, but his tone was calm and reasoned when he answered her.

"Don't worry, Henry Hayes knows how things stand between me and your precious military commander, he's the man's godfather. Why do you think I wasn't told the names of your senior staff prior to arrival? As for what happened between us, you obviously know less about him than I do. Ask John sometime why his mother died alone."

With that final, flat statement, Colonel Matt Sheppard, retired, spun on his heel and left.

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The next morning...

Waking up this time was slow as John floated through each layer of consciousness back toward the bright world. There was no urgency this time, no panicked heart beating frantically, no hand scrambling for a weapon, no dread that the restoration of his life had all been a wishful dream. He wasn't sure how long he'd been asleep, but he felt great, rested, healthy. His mind was content to float along, no longer scrambling from one fragment of thought to another, chaotic, uncontrollable. Beckett had been right when he said some uninterrupted sleep would be able to work wonders. He only remembered a handful of nightmares, and none of them had gotten as far as actually waking him, being soothed away almost immediately by familiar voices telling him he was safe. He was even hungry! Maybe the kitchen had some of the Athosian spiced soup left? Or- Hey! Supplies had just arrived from Earth! A fresh apple or orange would be perfect.

First thing was to get his body moving, though. Sleep, unfortunately, was unlikely to have cured the lingering soreness and bruising from his captivity nor the nasty wound to his left arm. Surely Carson had left him some painkillers to help. It was only as he contemplated stirring that he became aware enough of his surroundings to note the stillness.

Not to mention the hauntingly familiar agitated buzzing.

"Wha-"

His barely coherent mumble received an urgently hissed answer from Rodney.

"Sheppard! Don't move!"


	11. Ch 10: A Time for Truth

Disclaimer: Stargate: Atlantis and all characters therein are the property of MGM. This story is for entertainment only and the author is in no way profiting from it, nor exercising any claims to Stargate Atlantis.

Title: A Time to Heal

Author: Pyrodragon2006

A/N: Thank you so much to all who review, as always!

Chapter 10: A Time for Truth

"_Sheppard! Don't move!"_

His tone of voice instantly told John that Rodney was deep into outright hysteria. Still only partially awake, the colonel tried to decide why his latest nightmare about an iratus would have his friend in such a state until his mind put an external location on the buzzing noise.

About two inches from the colonel's face, with a corresponding weight seated on his upper chest!

It was suddenly all he could do not to allow himself to descend into a mindless panic deeper than Rodney's.

"Get. It. Off!"

Gritted teeth, beads of sweat materializing on his forehead, and a frantically beeping nearby heart monitor all betrayed his slipping control even as the phobia rooted him in place, unable to move. He could feel his fingernails cutting into the palms of his hands where he involuntarily clenched them, the pain actually helping to re-ground him a bit. Frantically, he squeezed already shut eyes tighter, knowing if he opened them, confirmed what he already knew was there, he'd lose what little of his normally iron will remained. If that happened... He had to stay lucid, for Rodney's sake if not his own.

"And just how do you propose I do that?!"

Rodney's voice had hit a high falsetto. Struggling to answer his friend, John also fought to slow his increasingly rapid breathing, aware that the more his chest heaved up and down, the louder the insect got.

"Don't. Care. DO IT!!!"

His lungs were screaming that he wasn't getting enough oxygen, though he knew he was close to hyperventilation. Tears sprang to his eyes as he awaited the agony of the thing latching on to him, knowing he could do nothing to stop it. More voices abruptly entered the room, loud, angry, frantic, but he couldn't break his mind away from the bug long enough to decipher what was said until a Scottish brogue over rode the others.

"Bloody hell! Get that thing off him! John, I need ya to listen to me, son. We're working on getting the iratus off, but I need you to slow your breathing down. Concentrate on my voice, colonel..."

Carson kept talking, trying in vain to keep the other man calm, but John found himself tuning into the frantic conversation nearby.

"Maybe hit the thing with one of Sheppard's golf clubs?"

"No! You wanna get that close?"

"We must do something _now_!"

"Fine."

"Ronon! What are you-?!"

A familiar whine, which had never sounded so good, so welcome. The insect _shrieked, _the sound drilling through John's head even as the weight left his chest, a thud sounding off the wall of his room as the bug impacted.

John didn't open his eyes to look, though, too preoccupied with the odd tingling sensation taking over his body, spreading outward from his chest. The panic that had consumed him moments before was gone completely, his mind strangely detached, floating at one step removed from everything occurring, even his own emotions. A slight jarring of the bed near his hip signaled someone sitting next to him, his eyes idly sliding open to ascern their identity as he attempted to puzzle out just what he was feeling. Carson.

"Hey, doc, what'cha doin' here?"

With a slight smile, he greeted the other man, noting his own slurred speech with amusement. This wasn't quite an alcoholic buzz. Nope, more along the line of being doped up on something that provided a slightly loopy side effect, kind of like... He gave a short, breathy laugh, which had Beckett pausing in his exam to stare at him.

"R'dney on morphine!"

It was becoming more difficult to speak, which almost broke renewed panic through until he realized his mouth was simply going numb. Huh. Weird.

"I thought you said the critter didn't bite him, Rodney."

Carson flashed his penlight full in John's sluggish eyes, causing the colonel to squirm, not sounding at all happy as he questioned the astrophysicist.

"I- It didn't! At least, I don't think- I don't know, I was a bit busy at the time! And what _about _me on morphine?! I swear-"

"McKay! Shut up. Sheppard caught part of my shot, doc. Bug moved on me."

Ronon seemed to be a tad miffed about that. Probably more because he'd almost missed than because he'd hit his CO, John decided. Wait a minute! Ronon had just _shot_ him! Again!

"Alright, that makes more sense, thank you, son." A pause and John watched idly as Carson leaned over him, gazing at something across the room. "Somebody get that bloody critter outta here before the thing wakes up again!"

"Well, don't look at me! Nowhere in my job does it say 'exterminator of steroid-overdosed ticks'!"

Rodney's response provoked several smiles, including a slightly numb one from John.

"The Ancestors forbid we even think of it!"

The colonel could picture Ronon's scowl as the Satedan most likely growled that very close to the scientist's face. The friendly teasing reassured John that his team was fine, just unhappy and letting off steam from the scare.

"I will remove it and report what has occurred to Dr. Weir."

Teyla, ever the diplomatic peacemaker, quietly taking charge of whatever needed to be done. Secure in the knowledge that everything was being handled by his family, John quite battling the effects of the partial stun and allowed himself to slip into sleep.

Noting the change in heart rhythm as his patient settled back into rest, Carson slowly removed his stethoscope and sat up, relieved. He had seen the terror on the colonel's face before Ronon stunned the bug, noted the tremors rattling the slim frame from head to toe as well as the sheen of sweat on his skin. Carson had been positive John would descend into a full panic attack, or worse, complete shock, but instead the colonel was relaxed back into the all important healing sleep he needed. Noting blood on John's hands, he gently turned them and bit back a pained moan. Both palms had four crescent shaped cuts where the man's fingernails had been driven into the skin.

"Oh, son..." He murmured sadly.

"Carson?"

The choked squawk from next to him reminded the physician of the two others waiting as close to the bed as they possibly could. Looking up even as he carefully began cleaning John's hands, he smiled reassuringly.

"The two 'o you better start breathing again before you faint."

Carson shook his head slowly in amazement, watching Rodney's bright red face slowly begin resuming a normal flesh tone. Ronon simply snorted, having momentarily still his breathing at the doctor's soft exclamation.

"He's fine, its just the effects of the stun, which was actually a wee bit of a blessing. Kept him from havin' a panic-"

The door sliding open behind him cut Carson off as Elizabeth, Lorne, Teyla, and Matt Sheppard filed silently in, causing the room to feel crowded.

"As I was sayin', the shot kept the colonel from going into shock, which is good, so long as it isn't simply delayed. The critter itself didn't touch him. He'll be fine with more rest."

Apprehension and worry faded from the group at the doctor's words, though Carson himself couldn't help reflecting on what might have been. This whole fiasco could have turned out much worse had John's luck not held yet again. The memory of last time, of being stuck listening, helpless, as a conscious man ordered his own heart stopped still haunted him. How much more could even John Sheppard take before he broke, physically and mentally?

"You're saying the iratus bug just sat there and didn't even try to bite John?!"

The startled question from the expedition leader grabbed everyone's attention. She was right, the insect had a tasty meal right there and another, in the form of one hysterical scientist, only a few feet away. Granted, when Carson and the other two members of the colonel's team arrived at their leader's quarters, the thing looked to be contemplating going after Rodney. Thoughts racing, Carson turned back to wrapping his sleeping patient's hands.

"No, it didn't, and the first one was leaping at you, Elizabeth, not to mention let go of the colonel."

"It found its way to Sheppard's office!"

Rodney blanched at the realization, face so twisted that for a moment, the Scot feared he'd need to borrow the colonel's wastebasket. Wouldn't be the first time Rodney's emotional reaction turned to a physical one.

"I'm going to run some more tests and blood work as soon as John's up to it. Might be as simple as some type of marker left in the blood, similar to what that Tok'ra left in Colonel Carter."

"Simple?! He's attracting the things, Carson!"

The mercurial scientist now had his arms crossed, glaring at the other man in challenge. The doctor grimaced in answer, doing his best to hide his other, darker fears. More than likely, it was his nerves talking, but what if the iratus hadn't fed because it sensed something wrong with its potential victim? That truly didn't bear thinking about, let alone suggesting aloud.

The truth was that everyone in the city relied on John, probably more than the man knew, a fact that had been made painfully clear last week when they were certain they'd lost him. Elizabeth had been sunk in her own private hell, alone in her office, but Carson had walked the halls, had seen the shock and grief ripple through the city as the news of what Kolya had done spread like wildfire. Rodney may have been the brains of the city, pulling scientific miracles to save the day, and Elizabeth the politician, turning enemies into friends, but John Sheppard was the heart and soul of Atlantis. He was the child, eyes lighting up the room with each new discovery, the optimist, bringing up the spirits of all when the seemingly impossible faced them, and, perhaps most important of all, he was the solid, steady rock who gave them the courage and strength to keep going.

"Any ideas where that thing came from, Rodney?"

Elizabeth had noted how Carson went a shade paler, obviously lost in his own thoughts as he tended to his patient, but stayed focused on the problem at hand. Time enough to sit down with some tea and drag it out of the doctor later. Hugging herself, she hid the shudder that ran through her as she glanced at her sleeping military commander. She couldn't imagine the terror he must have felt, waking to find one of those things not only in his room but _on _him! She'd have to meet with Kate and Carson, discuss how they'd approach this whole thing and any potential problems that might develop, not that John would easily admit to them. Rodney's loud 'harrumph' broke her from her thoughts.

"How the hell should I know?! Ronon and Teyla went to get breakfast for everyone while I went over more data from Radek. I look up, and that _thing_ is sitting on Sheppard like some big, life sucking blob! Ask Conan over there, he's the expert tracker!"

A hand flapped in the direction of the Satedan warrior, who was prowling the perimeter of the room, sharp eyes darting over everything. A grunt.

"I'm looking, McKay. There's an opening near the ceiling above Teyla. Don't see any other way unless someone opened the door."

A pointed, thunderous scowl aimed was aimed at the scientist, who had begun tapping at the computer on John's desk the moment Ronon mentioned an opening. Irritation flashed across Rodney's face, but he didn't look up from his work.

"I'm not deaf, you know, I would have heard the door opening!" The astrophysicist snapped back, then his expression tightened and he straightened up from the computer. "According to the city maps, that opening is part of the central life support system for Atlantis when in space. The bug could have come from almost anywhere."

"Would the creature not have been picked up on the city-wide sensor?"

Teyla frowned, brown eyes flicking from the hole to the bed's occupant. McKay heaved a put-upon sigh.

"No, because we don't normally have any reason to scan for anything that small and setting the sensors to that level all the time drains too much power. We ran several sweeps yesterday, which were clean, but there are any number of reasons the bug might not have shown up."

Well, absolutely no answers there, something that was really beginning to grate on their nerves. Twice with no leads- two times too many, especially as John was the one being targeted.

_"Dr. Weir! Rodney! We have found something!"_

Radek's excited voice burst over the com, accent heavy. "Are you somewhere I may show you?"

Elizabeth hesitated just a moment, unsure if having Radek come there could disturb the colonel. He needed as much rest as he could get, but... She tapped her com.

"Acknowledged, Radek, just a moment. Carson? Should I tell him to wait and we'll come to him or can he report here where we can all hear it?"

Just behind the doctor, John hadn't stirred at their quiet deliberations, pale, strained face turned toward them on the pillow. Heart monitor leads trailed from the top of the scrubs he still wore, that alone telling the Atlantis leader that her military counterpart wasn't well. Normally, the first place John would have gone after slipping from the infirmary yesterday morning was his own room for regular clothes, yet he'd shown up at her office still in the infirmary attire, and now still hadn't changed though he'd been resting in his own room for over twenty-four hours.

"Have Radek come here, lass. I'd rather not leave the colonel and the regular conversation seems to be reassuring to him somehow."

Good enough. She tapped her ear piece again.

"Come to Colonel Sheppard's quarters, please, Radek."

_"I will be there momentarily. Zelenka out."_

A thick, uneasy silence descended on the room, the medical equipment sounding disturbingly loud in the small space.

**_Crash_**

The sharp sound of glass breaking had Elizabeth spinning around just in time to have Rodney barrel into her, knocking them both to the floor. The breath exploded from her lungs, stars erupting in her vision, chest burning with the attempt to suck in oxygen. Hands lifted her limp body, massaging her sides gently to release her cramping diaphragm.

"Easy, easy. Don't fight it, love, you just had the wind knocked out of you, that's all. Rodney's a wee bit jumpy."

A very embarrassed Scottish brogue sounded in her ear even as sweet air trickled into her abused chest and her vision began to return.

"Oh, and you didn't, Carson? I saw you covering Sheppard! Besides, Conan and Xena had their weapons out, too!"

Rodney's eyes were still wide, face pale, and Elizabeth realized that the team must have mistaken the sharp sound for another attack, covering those most vulnerable. Which flattered her, really, since when the expedition first came to the Pegasus Galaxy, she'd never expected to see the day that Rodney McKay would put himself between another and danger. She'd lost count of how many times he'd done it now.

"What happened?"

"Nooo..."

The low moan was of such pure emotional agony that it stole away the diplomat's newly recovered breath for a moment as they all looked to the source, Matt Sheppard, kneeling by the dresser. There, on the floor, was the obvious source of the sound that had so startled them all- a photograph of two women, mother and daughter by the age difference and similarity of features. Matt was gently, almost reverently, brushing away bits of glass from the broken frame, fingering a small slash in the portrait itself.

A soft inhalation, half sob, jerked Matt's head up to look past Dr. Weir toward the figure on the bed, and for one instant, he met his son's eyes-

_Heather's eyes _

-finding there a depth of pain that surpassed even his own-

_Her son, **my **son_

-then the walls built of thick anger slammed back up within each of them, both hastily turning away

the other. But not before Matt saw one tear, a crystalline sparkle in the light coming from the window, roll down John's cheek even as his son once again began losing the battle with his body to stay conscious.

_Heather's hazel eyes, so beautiful, normally so full of joy and mischief, now closed forever, practically the only part of her body still recognizable under the gauze and medical machines. Gone forever, without him there, because of one young man. _

Bitterly, he ignored the young colonel, ever so carefully freeing the photograph from the debris and placing it face down on the dresser. He hadn't missed the fact that it had been on the wall in a location easily seen from the bed but not likely to be noticed by the casual visitor. At least, until he'd knocked it off the wall by accident.

"Who...?"

Matt glared stonily at Dr. McKay the moment the question started, causing the man to trail off uncertainly, suddenly nervous. None of these people would leave well enough alone, constantly prying at his history with the their precious military commander. Fine. Maybe if they knew, it would shut them up for a while.

"I didn't... You don't... Forget I asked."

The apprehension slapped at Matt and he mentally cursed himself for once again losing control of his emotions around these people. While on active duty, he had often been called Colonel Steel behind his back because he never allowed emotions to show, an ability he seemed to have lost the moment he set foot in this city. A deep breath and the anger dropped behind his normal impassive mask.

"My wife, Heather, and daughter, Melissa, Dr. McKay. They were killed in a carjacking four years ago. Melissa was shot and killed instantly. Heather was thrown from the car on the freeway, her injuries were too extensive for her to survive. She died a week later in the hospital, waiting in vain for her son to return from Afghanistan."

The other man's mouth quirked in a silent 'Oh'. Before anything more could be said by anyone, the Czech scientist with the perpetual bed head busselled into the room, saving Matt from any unwanted and probably insincere expressions of sympathy.

Rodney, meanwhile, had to keep from snapping at his colleague for the timing of his interruption. Not only had Radek destroyed any chance they had to get more information out of Matt Sheppard, but why couldn't he have come in earlier when the retired colonel was giving him looks that could kill? Especially since when the astrophysicist had seen that familiar glare on the face of John Sheppard, the man's son, it was usually followed by large amounts of _actual _killing?

Come to think of it, though, he'd learned more about his friend and team leader in the last few days then he had in the previous two and a half years. And how had he not noticed that photograph on the wall, even tucked into the shadows the way it was? Every time he dared to think he had neatly labeled the damn fly boy, the man sent him another bad puck pass from the nose bleed seats!

"What do you have, Radek?"

Elizabeth's calm inquiry jerked Rodney's mind back to the present in time to see the Czech give a quick negative shake of the head.

"It was not me, Dr. Weir. Dr. Malenkov discovered that the Jumper logs had not been reviewed from their last return after visiting an iratus planet. They came back during Lucius." Winces all around at that one, though Matt looked confused. Radek, however, continued before Rodney could jump in with an explanation. "Atlantis automatically scans all returning Jumpers to ensure there is nothing hazardous aboard, but we must review the findings, yes? This was not done, and there were two of the creatures aboard."

Quickly, Zelenka tapped on his PC tablet, then swiveled the screen around to show a diagram of a Jumper, two small blinking red dots clearly shown up in the cargo nets.

"You are suggesting two of the creatures returned to Atlantis over three weeks ago? Why would they not have been seen before appearing near the colonel?"

Teyla's question received several nods, though Zelenka was already shaking his head.

"Dr. Malenkov believes the creatures can become dormant for long periods of time. Perhaps that was the case here. However, it means that another bug is loose in the city."

Rodney fixed his assistant with a whithering look.

"We've already found it, or rather, it found the colonel. Try to keep up, here, Radek. What did you do with the thing, anyway, Teyla? Don't tell me its still alive somewhere in the city!"

He could feel panic surging through him at the thought, frantically peering into the shadows around the room. After all, if the thing found Sheppard once, it could do so again, and this time it might not be so picky about its meal! A calming hand on his shoulder and the slight smile on the face of his team mate stopped him from continuing frantic gibbering.

"Relax, Rodney, I immersed the creature in salt water, then Captain Zhukov took the body to be sent through the Gate to one which is in space. It is gone."

If it were anyone other then Teyla, he would have suspected he was being mocked for his fears, but the Athosian sounded sincerely concerned.

"Sounds to me like you found your explanation for all this. The bugs were pure carelessness on the part of base security. As for the attack on me, I rather publicly stepped on a few toes when I first got here."

The contemptuous tone made it clear what Matt thought of such people, not to mention the base security protocols. Rodney found himself bristling, though, since even he was able to pick up the hidden slap at John in the statement.

"All right. I still want everything checked before I sign off on this as an accident. Major, that means I'd like you and Teyla to interview the personnel who were on that mission, make sure we aren't missing something. I'll speak to Colonel Sheppard about any possible changes needed in security protocols when he's up to it. Thank you, everyone, for all the work on this. Matt, I believe we were going over some mission reports, would you care to continue?"

"Good. Maybe now things can get back to normal around here and I can get some work done."

Rodney called after the Atlantis leader as she and their guest as they left the room, then he turned back to the others with a sour grimace. It was met by an identical look on the face of his Satedan team mate.

"Something isn't right about all this."

The scientist rolled his eyes at Ronon's dry comment.

"No, ya think? Radek, I want you and I to go over those sensor readings with a fine tooth comb. I don't trust Malenkov as far as you could throw her."

"Rodney, why would you wish to comb a computer?"

Teyla's innocent question met with strained laughter from Lorne, Rodney, and Carson.

"Its an expression, lass. Rodney means he's going to be very careful."

"Ahh." Teyla left it that. It was certainly not the first time she'd been tripped up by one of her friends' odd sayings, and they all knew it wouldn't be the last.

"Listen, why don't you get started on that, doc, and let everyone know if you find anything. I'm going to keep security heightened at least until I talk to the colonel tomorrow, maybe have some of the marines keep a quiet tab on Dr. Malenkov's whereabouts. At least this way the colonel can get some more uninterrupted rest."

TBC... Hmm... Are you sensing lots and lots of trouble ahead?


	12. Ch 11: A Time for Hate

Disclaimer: Stargate: Atlantis and all characters therein are the property of MGM. This story is for entertainment only and the author is in no way profiting from it, nor exercising any claims to Stargate Atlantis.

Title: A Time to Heal

Author: Pyrodragon2006

A/N: Thank you so much to all who review, as always! You guys make my day!

Chapter 11: A Time for Hate

Late the next morning, John sat in the mess hall, grimacing as he pushed scrambled eggs around his plate disinterestedly, the things fast cooling to inedible. Seated at a table tucked into the far corner of the room, he'd so far gone completely unnoticed by the other occupants of the room, which was fine with him. Well, almost unnoticed. There _was _the small matter of a watch dog, currently one of Lorne's team, who was trying desperately not to be seen by the colonel and failing miserably at it. John just sighed, stabbing at the mess on his plate.

He'd woken this morning feeling relatively human, if a bit amazed at having slept almost forty-eight hours straight. His good mood, however, had disappeared instantly upon learning the iratus bug hadn't been a bad dream, nor was his father being here. Proof of that had come when he saw the unframed photograph lying face down on his dresser, a chill running through him at the memory of the cold hatred in Matt Sheppard's eyes. Not wanting to face the emotions associated with any of it, John had gritted his teeth through his team's offers of sympathy and support, quickly changing the subject.

After that, all three of them had tripped over each other in their explanations of the iratus bugs and where they supposedly came from. Not that John believed that all too convenient answer for a moment, and strongly suspected they didn't either. A suspicion that was confirmed when all three insisted on escorting him to his check-in with Beckett. Teyla was distracted, constantly scanning the halls, Rodney jumped at every sound, and Ronon fingered his gun the whole way. Back to normal. Yeah, right. When John used his medical with Carson as an excuse to send them packing, he hadn't been too surprised to catch a glimpse of his current shadow out the infirmary doors not long after.

Fortunately, Carson had been remarkably light on his warning lectures this morning, apparently picking up on his patient's mood. The doctor hadn't even remarked on John wearing his uniform, confining himself to simply eying the garments in disapproval before sternly reminding the colonel to take things very slow and easy today. Though that would change quickly enough if the doc caught wind of his lack of appetite, hence his hiding out in the corner alone.

With a sigh, he gave up on the food and turned his attention to the proverbial chimera in the corner- Matt Sheppard. There was simply no way he could avoid the man for long, not and do his job. And he _would not_ allow the man to stop him from returning to a normal life. Now more than any other time, John needed to feel a part of Atlantis again, to put Wraith and iratus behind him. To his dismay, even thinking of the creatures set his hands to shaking so badly he dropped his fork. Quickly, he balled it into a fist in his lap- or at least as much as the light bandage let him.

"Damn it, John, its over! Stop it!"

John ducked his head in embarrassment to hide his self-admonishing mutter. The last thing he wanted was someone seeing him and deciding their military commander had cracked under all this. He laughed softly at himself. At least he hadn't thought about Kolya or his Wraith lately! Though...

Absently, he rubbed his good hand over his sternum, where the Wraith had both taken and returned. He'd heard more of his team's discussion yesterday than they thought, he heard the speculations on why the bugs were seeking him out.

_...brother..._

No! He would not hear that rasping voice any more!

"John? Are you all right?"

A hand on his shoulder had him jerking away in startlement, heart beating wildly, then jumping as his juice glass tumbled to the floor, breaking with a sharp crack. Looking up, John met Elizabeth's wide eyes and settled back into his seat, flustered.

"Damn it! I-ah... Sorry, Elizabeth, I didn't hear you."

John forced himself to take a calming breath, not too surprised to see his father standing behind the Atlantis leader. One disapproving look was all it took to have John jumping to his feet, headed for rigid attention before his brain overtook instinct and he relaxed slightly.

"Good morning, Elizabeth, sir. Forgive me for being unable to greet you upon arrival."

A not quite apology observed for the sake of form and peace on Atlantis, though his tone was cold, dead. In his head, John provided himself with the unspoken meaning of his words even as hazel eyes met green, acknowledging the firing of the first shot.

_I'm glad I didn't have to stand there pretending to be polite._

"Quite all right, Lieutenant Colonel. I understand your wound was rather severe."

_Translation: Buck up, kid, you can't fall over just because you're bleeding a bit._

How many times had he heard that growing up? He'd lost count by the time he was ten, insisting he was perfectly fine with a nasty gash in his head and a concussion from falling off his bike. There were times having a naturally high threshold for pain came in rather handy. After being thoroughly told off for jeopardizing the life of his son by the base doctor, the colonel had begun to believe him when John claimed he was hurt. Now, though, that cynical tone was back.

A gentle clearing of the throat behind him snapped his attention from the past to see the two young marines detailed to KP duty standing there with clothes, mop, and bucket, gazing nervously at the floor behind their CO. The area full of broken glass and orange juice, threatening to send anyone walking by to the floor themselves. John winced, giving them a slightly rueful grin.

"Right. Thank you, gentlemen. Dr. Weir, Colonel, I was just headed out. Was there something I could help you with?"

An eyebrow went up at his formality, but Elizabeth gestured him toward the mess hall door.

"Yes, John, there is. I was about to give our guest a long overdue tour of the city and wondered if you were free to join us."

She knew very well Beckett wasn't allowing him to do much of anything, so he highly doubted Elizabeth would take 'sorry, I'm busy' as an answer. Inwardly, John's gut clenched, stomach rolling, making him glad he hadn't eaten anything as his mind worked furiously at deciding how to handle this. She must have known they couldn't avoid one another, so she was chaperoning! Outwardly, his face was carefully fixed in a polite, slightly good-humored mask.

"I am. Dr. Beckett's allowing only light duty until my arm heals and they ensure there are no hidden aftereffects of..." He paused for a long moment, searching for words least likely to set off more nausea. "My captivity. Where would you like to start?"

_Something_ flickered for a brief moment in the depths of the elder Sheppard's eyes at his calm answer. Sadness? Compassion? A horrid thought struck him as they walked slowly down the corridor toward the gyms, Elizabeth leading the way. John froze in misstep, looking like a player of the old children's game 'red light, green light', the other two continuing on for a few steps before realizing they'd lost him.

"John? Is something wrong?"

Puzzled, Elizabeth reached for his good arm, only to have him jerk away from her hard, eyes snapping in turmoil.

"You taped Ko- the transmissions, didn't you?" His anger, at himself, her, he didn't know, mounted as he stumbled over the Genii's name sticking in his throat. "You showed them to the Colonel!"

Matt faced him, speaking in a soft tone John hadn't heard since his Mom was alive, though there was a hint of a hard edge to it.

"She did. It was worse than anything I've ever seen. How did you manage to get taken, anyway? I didn't have a chance to go over that section of the report."

John grit his teeth angrily at the mental translation of that one.

_How could you be that stupid?_

His face hardened, tone clipped and factual.

"I trusted someone who was supposed to be an ally. They walked us into an ambush. I had rear guard as my team retreated to the gate."

_Translation: I was doing everything by your precious book, so stick it._

Elizabeth must have caught some of the nonverbal byplay on that one, frowning in disapproval at both men.

"I ordered Colonel Sheppard's team on the mission. Our alliance with the Genii is fragile at best and not an obligation that can be taken lightly. Unfortunately, hindsight is always twenty-twenty, but new precautions are being put into place on both sides of the alliance."

_I'm the boss and if you have a problem with one of my people, you talk to me._

John's expression darkened, about to object when she shot him a fiercely quelling look. Apparently chivalry went both ways on Atlantis. Matt, on the other hand, seemed perfectly willing to take on both of them.

"I'm simply trying to understand what happened and how the chain of command works around here."

Said with what appeared to be a placating smile, that one needed no mental translation. Mr. Innocent his father was not, though he was making a damned good attempt to seem that way, John decided. A brief dizzy spell had him leaning against the corridor wall for support, unable to push through as he normally would have, waiting tensely for the inevitable snide comment on weakness. Only this time it didn't come. Pushing himself away from the support, he found the man pensively watching him instead.

"John, maybe we should-"

He was already resuming their walk toward the gym, forcing the Atlantis leader and the retired colonel to scramble to keep up.

"I'm fine, Elizabeth. Carson warned me that the antibiotics could cause a few spells. Let's just-"

A raised hand cut him off as she stopped, triggering her com.

"Weir."

Her face darkened at whatever she was told, but the diplomat quickly clicked back off, eying both Sheppards.

"I have to deal with something. John, are you all right to continue without me?"

John leaned back against a wall, considering the question for a moment, certain she meant more than his physical health. Being stuck with the Colonel all day wasn't exactly his idea of rest and recuperation, but he also knew Elizabeth had been running herself ragged lately. This, at least, was one thing he could take off her shoulders and they would be in public areas, so Matt was unlikely to start any knock down, drag out fights between them.

"Go, Elizabeth, we'll be fine. Let me know if its anything I can help with. I think we'll just go down and see how Ronon's doing with the latest batch of marines. One of them should've been stupid enough to challenge him by now."

That received a smile, her body relaxing as he'd hoped it, both of them having witnessed the Satedan puncturing military egos more than once. Even better, she turned and hurried away without questioning him further or allowing her eyes to stray to his chest. John's returning good mood, however, vanished with the hand on his elbow tugging him toward a nearby balcony and a cold voice in his ear.

"We need to talk."

As the ornate stained glass doors swished closed behind them, John jerked away from Matt's grasp, thinking sourly that he should have known better. He knew the other man wouldn't be allowing him to duck this again, either. Colonel Matt Sheppard was used to getting what he wanted when he wanted it. Looking out over the ocean, he pulled together what shreds of calm and control he could, slowly turning to face the man he'd once called 'father'.

"About what?" A deliberate pause. "Sir?"

The hesitation before the honorific was a petty form of contempt, but it was about all he had in him at the moment. Unfortunately, Matt had never been the type to pull his punches.

"I thought you were still hiding down in Antarctica."

The emphasis on the word 'hiding' caused John to flinch, once again moving to lean on the rail, his back to the other man.

"I could be useful there and you'd made it pretty damn clear you never wanted to see me again. It sounded like a good idea at the time."

His tone bitter, and a little bleak, he blinked back the burning in his eyes, not allowing it to turn into the threatening tears as events he thought long buried were forced back to the surface of his memory. A derisive snort came from behind him.

"I'll bet. I can _almost_ understand your defiance of orders, we don't leave our men behind."

John's fingers curled hard around the railing in pure astonishment before whirling to face Matt, his own anger rising. He'd had it with the whole situation, tip toeing around the older man in his own home. If the Colonel wanted to have it out with him, fine, he'd give as good as he got.

"Then what the hell are you so angry with me for, if not your precious rule book?! You made sure the brass wouldn't even..." He broke off for a second, overwhelmed by grief and rage. "They wouldn't even let me go to Mom and Mel's funerals!" Matt met him glare for glare, but this time John wouldn't back down. "You shut me out, refused to say a word! What the hell was that?!"

"What was that? You _betrayed _your family then ran like a coward first chance you got!"

Eyes blazing, jaws clenched, hot hatred and rage coursing through them, the two men stood just inches apart. Instead of yelling now, however, their voices had both dropped to frigidly cold, angry tones, soft, marking both men at their most dangerous.

"How long before you run from this place, too, John? They talk about you as if you were their hero, you know, invincible, no problem so big you couldn't save them. How long before they see how soft and weak you are, unable to face the painful choices? How long before they see the _truth_?"

"_What _truth?!" John spat back at the other man, hollow pain echoing the words inside him. "That I can't save everyone? They already know that and at least I _try_! You know damned well I didn't run!"

A harsh bark of laughter.

"What do you call it, then, because that's sure as hell what it looked like to me! Going off on some half-assed rescue attempt that command was already working on, trying to look like a hero instead of facing your fears and coming home to be with your mother as she died! Do you have even the slightest idea how much you hurt her? That's all she was hanging on for, to see you! And what about _me?_ I was waiting at the base for a plane you weren't even on instead of being with her when she passed! My own _wife_! Do you even care how much that hurt?!"

John just stared at his father, cold shock coursing through him so violently it physically hurt. Knees threatening to buckle, he opened and closed his mouth several times, trying to force out words that refused to come. Matt just stood and stared at him, and John was shocked to see hatred and soul deep grief plain on the normally cold man's face, one tear tracking its way down his cheek. A loss as deep as his own. Finally, as the Colonel turned away in dismissive disgust, he was finally able to utter a half-angry, half-devastated whisper.

"They didn't tell me... Not until I got back..."

All color drained from Matt's face as he spun back to his son, collapsing heavily on a bench, legs as shaky as John's own. He looked like someone who'd just had their whole world pulled out from underneath them, as Ronon had when he saw the MALP video from Sateda. _That_ mental comparison rekindled the rage in the younger man as he finally understood _why _his only surviving family had so completely turned his back on him.

"Did you honestly believe I could do that to _Mom_?!" The guilt that flashed across Matt's face was crystal clear, a punch to the gut for his son. "You did."

John whispered before pushing past Matt, sick at what he'd just learned, desperate to be far away from this man he'd once trusted and revered. Head bowed, stride firm to prevent anyone from questioning him, he headed for the one place he could think of to be undisturbed right now- the Jumper Bay. A couple of quick turns, a mental nudge to a transporter door, and a slightly longer route dealt with his unwelcome shadow, and he slowed his pace a bit, deep in thought.

It _hurt_, what his father had believed of him, like a knife straight to the heart. John had worked so hard to build up walls, to keep everyone at arms' length with a smile and a joke, and he'd succeeded. Until he sat down in that chair in the Ancient Outpost, anyway. As he'd told Teyla in his fumbling, half-embarrassed way, these people had become his family in all but blood. The problem was he hadn't truly ever lost that piece of himself that still looked up to his father as the invincible, infallible, real American hero and wanted to be just like him. Now...

Exhausted, emotions at a boil, he barely registered the sight of the marine on security detail in the Jumper Bay laying on the floor before a poorly aimed Wraith stunner shot sizzled overhead.

"Shit!"

John swore under his breath as he dropped and rolled under the railing to the floor of the bay a few feet below. Impact with his wounded arm brought fresh tears to his eyes, momentarily freezing him in pain on the ground, which was all it took for his attacker to be on him. Noting through water-blurred vision that the other man had just grabbed John's nine millimeter, he brought a knee up hard into his opponent's solar plexus, struggling one handed for his weapon. As they fought, the gun came up toward John's head, his opponent pulling the trigger even as the colonel jerked on it...

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Matt sat staring after the departed figure, tears threatening to force their way to the surface. Suddenly, he whirled and clutched at the balcony railing, vomiting over the side, body shaking with anger, guilt, grief...

"Oh, Heather, what have I done?"

The forlorn whisper to the waves met with silence. Matt's conscience was more then willing to provide a brutally frank answer, though. He'd allowed his own anger and pain to blind him to the truth, lashed out against a young man whose only crime was following the principles his parents had worked so hard to instill in him. He'd destroyed his relationship with his only living child, perhaps irrevocably. Matt had to find John, now, force himself past that soldiers' facade, see if there were some way to begin repairing the damage.

Restless, he headed for what he hoped would be John's destination- the place where they kept the Ancient planes, whatever fool thing they were called. It was his best bet, since from the time John was small, he'd sought out the airfield whenever he was upset. No matter what base they moved to, first chance he got, John would be gone, scouting out a place to watch the flight line. Matt couldn't imagine his son had changed even that instinctual reaction.

"Where are _you_ going in such a hurry?"

The harsh interrogative stopped the retired colonel in his tracks, spinning to confront the man who'd been consistently hostile to him since the day he arrived, Dr. Rodney McKay. There were many stories floating around Atlantis about the self-proclaimed genius, both good and bad, but Matt hadn't had enough contact with the prickly man to know the truth yet. Right now, however, a member of John's team may be exactly who he needed, especially since he wasn't quite sure he was still going the right way.

"To speak with Colonel Sheppard. Someone saw him headed toward the Jump Bay, wherever the hell that is."

Actually, that John was there was a guess, of course, but the older man was hoping for some help, not an interrogation. He received a roll of the eyes.

"Its Jump-_er_, not Jump, and those are our ships. I'd better come with since not only were you about to head the wrong direction, but none of us trust you alone with him."

There was more truth to that than Matt cared to admit. The heated comment, however, had him instinctively bristling.

"Thank you, doctor, but I don't need a chaperon to speak with my own son."

The retired colonel snapped even as they headed rapidly down a different corridor. McKay gave a derisive snort, fixing his companion with an ugly glare.

"So he's your son, now, is he? You're worse than _my _parents! Let me put this in terms a kindergärtner can understand. I take you, or you go wander this city without a map and we see you sometime next year. Which is it?"

At that, Matt almost told the scientist where to stuff it in the crudest barracks language he knew. Completely enraging a member of his team, however, was not a recommended way to get John to listen to him.

"Fine. Let's go."

Several minutes of brisk walking in hostile silence brought them to the large bay...

Just in time to see a man with a gun standing over the body of John Sheppard, either unconscious or dead. Before either of them could say a word, the bright flash of a weapon enveloped them and both men slid bonelessly to the floor, unconscious.

TBC...


	13. A Time for Despair

Disclaimer: Stargate: Atlantis and all characters therein are the property of MGM. This story is for entertainment only and the author is in no way profiting from it, nor exercising any claims to Stargate Atlantis.

Title: A Time to Heal

Author: Pyrodragon2006

A/N: First of all I have to apologize for the inexcusably long time this chapter took me. Let's just say several illnesses in the family, lots of work, and a bridge collapsing right next to where I work only a few hours after I last drove over it are not conducive to overcoming writers' block. Thanks, everybody, for hanging in there with me.

And thank you to everyone who supported Minneapolis through thoughts, prayers, and actions following the bridge collapse on August 1. Its a sore that will never be completely gone, but you've helped us begin to heal.

Chapter 12: A Time for Despair

"Close the gate, don't let them through!"

Elizabeth shouted to the gate technician over the blaring of alarms, panic shooting through her at the sight of the craft preparing to leave. It had only been a minute since the reports of a security breach in the Jumper Bay had sent the base to high alert, though it felt like forever to the Atlantis leader. Once again, events were spiraling out of her control, her heart sinking as the sergeant next to her shook his head.

"The Jumper has control, ma'am, I'm locked out."

"Dr. Weir!"

Even as the small ship slipped through the event horizon, Major Lorne raced up the steps toward her.

"Whatever that address was, redial it! Now!"

"Do it!"

Without John here, she put her trust in his second without hesitation, giving the order. Some part of her noted the colonel's uncharacteristic absence during a crisis with growing unease, though John was still on medical leave. Next to her, the tech was rapidly hitting the symbols, sending the lights on the Ancient machine spinning. Elizabeth quickly turned an inquiring glance on Lorne, now standing nearby.

"If we can dial in fast enough, doctor, we can block the gate, keep them from going to another, unknown-"

The major broke off, swearing softly as the seventh chevron refused to lock, indicating that the other gate was already in use.

"What just happened, major?"

Elizabeth asked grimly even as the other members of the command staff began appearing, obviously having dropped what they were doing when the alarms went off. Gaze flicking from face to face, noting each person, the Atlantis leader felt another chill race down her spine. Teyla and Ronon, together as they so often seemed to be lately, then Carson... But no John or Rodney, just Lieutenant Patterson, a member of Lorne's team, with Zelenka a step behind him. It was the Czech who answered first, obviously having overheard her question.

"A scan of the Jumper picked up both Rodney and Colonel Sheppard aboard, along with three others!"

"And I've got two marines down in the Jumper Bay, looks like a Wraith stunner, along with equipment scattered and blood. Patterson! I thought you were supposed to be watching the colonel!"

Lorne growled at his young lieutenant, who cringed, guilt flashing across his features.

"I was, sir. The colonel went out on a balcony near the gyms with the as- presidential adviser right after Dr. Weir left them, sir. I heard some yelling, then the colonel came charging back in. He lost me when a transporter door closed quicker than it should have. That was less then half an hour ago!"

"We've already locked down all critical parts of the base, ma'am, and I just ordered all personnel to check in with their supervisors, so we should know if anyone else is missing fairly soon."

Elizabeth grimaced at herself as she automatically paused, waiting for Rodney's normal sarcastic 'Well, of _course _someone's going to be missing! Did you skip elementary math for grunts, major?' Hastily, she cleared her throat.

"Good, thank you, major. Let me know. Dr. Zelenka, Ronon, Teyla, help the major investigate the Jumper Bay, see if you can find out anything else. If whoever took them got hurried or interrupted, we may get lucky."

She turned away, leaning on the rail overlooking the now silent Stargate to hide the fear in her eyes.

Dr. Meredith Rodney McKay finally understood the phrase 'If this is what the morning after is like, don't tell me about the party.' His throbbing head was timed with the waves of nausea rolling through him, and both were underlain by the steady ache in the rest of his body. In short, it felt like he'd gone ten rounds with Sheppard... then Teyla... then Ronon. No doubt it was all their fault, too. With a mental curse, he started slowly attempting to straighten his limbs before he even thought of bothering to open his eyes and look around. Not that he needed to, since he already knew what he'd see. This type of awakening had become all too common since he'd met a certain insane fly boy and come to this backwater place. Nope, cold, hard floor killing his sensitive back, weapon gone, headache, they were in another prison, cage, jail, local tree hut, whatever. Mind fuzzy and sluggish, the astrophysicist tried to force up the memory of which planet they were on, but gave up fairly quickly. The scenario would have gone something like this- The colonel had smarted off to yet another oversensitive, dumb as a box of rocks native and gotten them all thrown into the local equivalent of a jail. Complete with a cold, hard stone floor sure to ruin McKay's very sensitive back, of course.

The rustle of someone moving around near him told the astrophysicist it was almost time to get up and break out once again; no doubt with the maximum amount of gun play and use of explosives by Sheppard, Conan and Xena. The only bright side to the whole thing was that the sooner they got out, the sooner Rodney could find the infirmary on Atlantis and Carson's painkillers! Lots and lots of painkillers.

"What the hell did you get us into, Sheppard?"

His grousing question was met with a brief silence, almost lulling the groggy man back to sleep...

"Excuse me?! What did _I _get us into?! This is your damned galaxy!"

The stranger's voice shot McKay's eyes open and he sat up, finding himself fighting hard to stop his spinning head and stay conscious. Hands grabbed him, pulling him backward until he was propped against an equally hard, cold wall and a cup was pressed to his lips. A cautious sip was rewarded with cool, only slightly metallic tasting water and he reopened his eyes to meet the grim green ones belonging to Matt Sheppard. Great, right family, wrong man.

"I'm going to assume that comment was directed at John, not me?" At McKay's nod, the man grunted, apparently satisfied. "Now that you're awake, Mr. Genius, why don't you get us out of here before they kill him?"

McKay blinked, sitting for a long moment, attempting to puzzle out what the other man had just said even as he absently opened and ate the Powerbar the other man gave him.

"Get out of where? Kill who? Where the hell are we?"

He leaned around Matt to assess the situation, swearing softly at what he saw. They were surrounded on three sides by the bars of a detention cell very similar to those on Atlantis and on the fourth by the solid rock wall McKay was currently using as a backrest. If this thing had a forcefield similar to the one on Atlantis... In pure, uncharacteristic frustration, McKay tossed his now empty cup at the bars as hard as he could. Childish, yes, but for once, it felt good. At least until the cup actually hit the barrier. Instead of just bouncing off and falling to the floor, this field sent it straight back at him at a highly accelerated speed, causing the astrophysicist to freeze in pure shock. At the last second, Matt Sheppard's hand shot out, slapping the offending object out of the air less than an inch from Rodney's nose.

"How have you lived this long, McKay?" Sheppard's sarcastic tone made it clear he thought as little of the scientist as McKay did of him. "Just get us _out _of here!"

Rodney rolled his eyes, knowing the gung-ho soldier definitely wouldn't be happy with what he was about to tell him.

"One problem with that, Sheppard, I can't! Now, what the hell is your problem?! Missing a chance to yell at your son?"

Sheppard went white, then red, rage written across his features, causing Rodney to scramble quickly toward the far side of the cell. The man was looking distinctly dangerous, leaving the scientist with no doubt that he would kill without hesitation to achieve his goal. Whatever the hell that objective was. The few times McKay'd seen John Sheppard with a look even half that cold, there'd been a lot of dead bodies around not long after!

"If you _ever_ say such a thing again, you'll learn the true meaning of hell, McKay! You haven't had to sit here and listen to him scream so hard I don't think he can make a sound anymore! Take a good look!"

A finger shot out, stabbing toward whatever was outside the cell behind the frightened astrophysicist. Rodney gulped, realizing he'd been so focused on their captivity that he'd failed to look beyond the cell or wonder where John was. He turned slowly, prepared for just about anything except what he saw. It was a scene straight out of his worse nightmares.

John was seated about ten feet from them, manacled to a chair like a bad rerun of what Kolya had done only a week earlier. This time, though, there wasn't a Wraith in sight, just iratus bugs, lots of them, crawling all over John, the area near him, and the cage McKay and the elder Sheppard were in. McKay's stomach lurched as he fell to his knees with bruising force, his body beginning to heave, expelling the small amount of food and water he'd just eaten. Sweat mingled with tears on his face, teeth chattering as he began to shake uncontrollably in response to his mind's revulsion. This wasn't a grainy picture being broadcast from some distant planet, allowing Rodney even the illusion of a separation. This was horrifically real and he was completely helpless to stop it! Hands steadied him until at last his body stopped even the dry heaves, then Rodney sank to the floor, heedless of the smell nearby, simply too spent to move.

"How could anyone do that? To him of all people?"

He whispered hoarsely, his eyes kept squeezed tightly shut, not caring that it was a man he considered an absolute jerk with him at the moment. How much more could this galaxy put John through before he broke? First Wraith, now iratus b- McKay's eyes flew open in alarm once more, forcing himself to sit back up so he could see his friend. The creatures were scurrying around, fighting each other for the positions actually touching Sheppard, but none of them seemed latched on and there was a pool of blood on one side of the chair that the iratus were carefully avoiding. One of the bugs, larger than the rest and buzzing in agitation, climbed up the colonel's chest toward his face, which, McKay noted for the first time, had a blindfold covering the trapped man's eyes. Wires trailed from Sheppard's clothes, leading to several alien monitoring machines, the design unfamiliar to McKay, and-

An Atlantis data pad with a broken shoulder strap sitting propped up against a half dissected bug. Movement from the chair drew McKay's attention back to his friend in time to see him thrashing wildly against his bonds, apparently attempting to dislodge his unwelcome seat mates. Sheppard's mouth opened, but no sound came out, leaving Rodney trembling in sick realization once again.

"He's conscious!" The astrophysicist glared accusingly at Matt, though logically he knew the other man couldn't do anything. "How long have we been here? Who's responsible? Kolya? The Genii?"

Matt met him glare for glare, but when John slumped limply in the chair once more, Rodney saw something he never thought to witness on the elder Sheppard's face. Compassion, worry, a hint of guilt, pain; not for himself but for the son he'd spent the last several days denying existed.

"I think he's only semi-conscious now." The other man's voice had dropped to a whisper. "They forced some drug down his throat about six hours ago. Bastards let John scream until his voice went, and you can see where the stitches on his arm have at least partially ripped. They brought him in about eighteen hours ago by my watch, just as I was getting over the pins and needles from whatever they shot us with in the Jump Bay."

"Jumper! Its _Jumper_ Bay, and it was probably a Wraith stunner." McKay rolled his eyes in annoyance as he continued to peer around the room. "Wait! Did you say eighteen hours?! I can't have-"

Matt shook his head.

"No, they gave you something, don't know what. As for who they are, I don't have a clue. None of the ones I've seen match the descriptions of Genii, though."

"And how the hell could you know that? Did they have signs around their necks saying 'I'm not Genii'?"

Rolled eyes and a snort of disgust.

"No, McKay, their eyes were bright red! Any other stupid questions or are you ready to find us a way out of here?!"

"And how would you suggest I do that? Ask them nicely? This is Ancient technology! When we tested it on Atlantis, not even I could find a way to escape! Basically, we're screwed and so is Sheppard!"

Matt grabbed Rodney's jacket, pulling the other man face to face with him.

"There's always a way, McKay, _find it_!!"

tbc... A lot sooner than this last one, providing life doesn't throw anymore stones at me.


	14. Ch 13: A Time for Regrets

Disclaimer: Stargate Atlantis and all characters therein are the property of MGM. This story is for entertainment only and the author is in no way profiting from it, nor exercising any claims to Stargate Atlantis.

Chapter 13: A Time for Regrets

Four hours later found McKay and Matt both slumped against the wall of their prison, eyes locked on John. The scientist had proven all too accurate in his assessment of their situation. Careful probing of the force field walls had shown no gaps, only earning Matt a slightly reddened, throbbing hand. No way to get at the control panel so tantalizingly in sight, no way to free John, no way out of this hell. Of course, McKay couldn't resist pointing out that the force field was the only thing keeping them from becoming the bugs' next meal, either, painting a disturbingly vivid picture of what the things were capable of in Matt's mind.

The advisor had read the reports about the things back on Atlantis, but that had been dry, factual, even as it spelled out the experiences of an anonymous officer on base slowly turning into an iratus-man thing. He'd had to admire the kid's tenacity, facing that yet still able to recommend that his superiors put the safety of the base first, even if it meant his life. Matt just hadn't realized it was John until McKay acidly informed him. He hadn't even been able to _look_ at the food the younger man was devouring after that, his stomach was so rocky.

"How the hell can you eat that with John- John-"

Matt broke off, gesturing vaguely in the direction of where his only living child sat, captive in the middle of yet another nightmare.

"I'm hypoglycemic, okay?" McKay growled, though pointedly looking away from his trapped friend. "The last thing that could help Sheppard is me passing out if we did get a chance to escape! What the hell do you care, anyway? Suddenly going for 'Dad of the Year'?"

Regret stabbed through Matt at the harsh, yet all too true words. If only…

"I was wrong, McKay. Is that what you wanted to hear?" He snarled at his cell mate, then slumped back against the unforgiving stone, voice dropping to a whisper. "I was wrong about John, and I don't know how to tell him, make it up to him. What I did…"

Beside him, he felt McKay stiffen.

"Yes, well… Acknowledging that you're an absolute moron would be the first step. And I thought my parents were bad. What the hell did you do, anyway? I didn't even know Sheppard's father was alive until you showed up!"

Matt bit back a less than civil response to that, tacitly conceding the other man the right to question so personal a history. As a member of John's team, this man had more of a claim to the title of 'family' then the older man did at the moment. He'd seen how close they all were, watched them give up whatever they were doing at one word from the doctor to stay with his son, help him in a way his father hadn't since John was a small boy. When Matt had begun trying to 'prepare' John for the military, treated him as he would a soldier under his command. How often had he seen John laugh and play, be a little boy, in his presence since that time? Only when Heather placed herself as a firewall between them or when John's interests outside the military intersected with Matt's own few vices, such as college football. It'd actually worked well when John was older, in the service. Matt related better to the younger officer than he had in years, even if he watched the young man, as Heather had put it, 'just waiting for one very human mistake!' Then…

"When the carjacking I told you about killed Melissa and Heather, John was serving in Afghanistan."

He kept his eyes focused on a distant wall, not wanting to see the reactions on McKay's expressive face even if the man had earned some claim on hearing this tale.

"I'd been against him going into the service, thought that maverick streak of his would get somebody killed. Probably not him, either. But John insisted and Heather backed him, said it was his choice. All the kid wanted to do from the time his was five was fly."

A soft half-snort, half-laugh from next to him met that statement.

"For a while, it looked as if they were right. John rose in the ranks quickly, proved he could fly anything with wings or rotors. That split second judgment of his, willingness to go where few others would lead to him being tapped very early as a Special Forces pilot, one of the elite. Which also put him in every war zone and hot spot around, flying missions that are still sealed? Then, a friend of his went down behind enemy lines. The brass was working on an extraction, but the base commander was known for being more concerned about how his own career would be stained by a FUBAR'd mission then by concern for his men. And our people didn't have a history of lasting long once the Taliban got hold of them. John went in, against orders and only with the thinnest chance of success. And, I thought, knowing that his sister was dead, his mother dying, her last wish to see him."

Matt paused, dropping his head onto his raised knees to hide the pain, the tears. An awkward hand patted his shoulder.

"Heather died while I waited at the base for a plane I'd been told John would be on. When he showed up out of the desert five days later, hauling the body of his friend and half-dead himself, I was furious. I ordered the doctors not to allow him home for the funerals, cut him off, never spoke to him or saw him again until I came here. What I didn't know was that the base commander never bothered to tell John about the- the accident. I let him- My own son-!"

He shuddered, an assault of emotions he'd not felt since that fateful day washing through him. The moment John had whispered those words on the balcony, he'd known what happened. Should have realized it four years ago, when Henry all but shouted it at him. The base commander hadn't liked John's style, his disregard for orders, but what was at the heart of it all had been a grudge against Matt himself. The sins of the father paid for by the son, as it were. If Matt wondered sometimes how O'Neill had risen through the ranks, he'd had no doubt how that jerk Crane had. Bastard wasn't even Air Force, he was Army! The man only had one notable skill, and that was making himself look good at the expense of those around him, even when he'd been the one to screw up. Or perhaps two skill, if you counted knowing whose backside to kiss. From Crane's early career in the military police attempting to re-capture the only men ever to escape Fort Bragg stockade on up, he'd left a swath of shattered careers and mud-spattered men of all branches in his wake. A run-in over a stupid move made by Crane in Panama during Operation Just Cause had led to Matt's own stalled rank, then early retirement. He'd just never thought the man would stoop so low as to go after John, especially using the deaths of family to do it. How could-

"YOU!"

McKay's outraged exclamation brought his head up as the physicist scrambled to his feet, standing almost touching the force field, body rigid in anger. One of the red-eyed, orange-tint skinned aliens Matt had seen earlier, a broad shouldered male, had entered the room, towering over the short, rather homely looking woman who walked in front of him. It was her McKay had snarled at, watching her approach with ill disguised disgust. Matt, however, frowned, not as interested in her as in the behavior of the iratus that had been nearby. The alien insects had taken up an agitated buzzing sound, quick to get away from the two who'd entered, even when it meant leaving their favorite positions on John when the man approached the bound man. He reached to check several devices attached to his son, his touch causing the young man to thrash, mouth forming soundless words of defiance.

"Leave my son alone, you sick son of a –"

Matt found himself mirroring McKay's enraged pose, snarling at the alien before he was even conscious of standing. The woman, whose eyes were a very human blue behind her thick glasses, curled her lip in contempt.

"I will do as I wish. My work has been delayed long enough by such _touching_ concern."

Her voice dripped sarcasm, accent unmistakably Russian. Matt just barely caught himself before he hurled uselessly at the cell wall, trying to get at her, make good his threat of a minute before. His speechlessness was not shared by the volatile McKay.

"H-how could you?! That's a human being over there! He's saved your life, he's- he's- You're insane! Let him out of there, Malenkov! NOW!!!"

The woman simply laughed, pleasantly amused by the astrophysicist's reaction.

"And why would I wish to do that, McKay? He has proven so very useful to us, pushing my research forward months in just a few hours. I am so close now! He will be thanked by millions, sacrificing for such a brilliant discovery!"

"Sacrificing!" McKay's voice rose in pitch. "Close to _what _brilliant discovery?! You're an entomologist, study bugs! Who's going to thank him, the cockroaches? I'm the one who saves the city, finds breakthroughs in power and Ancient technology. All I see over there is useless torture that makes you no better than the Genii!"

"Ach, that has always been your problem, McKay. Cannot see past your own overly large ego, and when you are one who would benefit so much from my research! Instead, you refuse to open your eyes, backing Dr. Weir and the colonel in their stupid restrictions. How am I to work without specimens, hmm? Test subjects? Dr. Beckett had no such problems! You do not even allow me access to the colonel's records, will not consider a few harmless tests. What is a little discomfort to a soldier? Is what they are paid for, da? Expendable!"

"I don't know who the hell you think you are, lady, but there won't be much left by the time I'm through!"

It was a useless threat at the moment, but Matt's rage could no longer be contained, not in the face of such blatant disrespect.

"Let us out of here! Now!"

He barked in his best command voice. Out of the corner of his eye, he noted John flinch hard, renewing his struggles at the sound of his father's shout. The boy was exhausting himself. Malenkov snorted, moving to stand directly in front of Matt.

"Soldiers! Always so arrogant, sure of their superiority over everyone. Do you not see, McKay? The Iratus may give life just as the Wraith does! The Klo'kan even call them 'Children of the Wraith', seek to learn their secrets as they have other races, including your precious Ancients. Imagine what minds like yours and mine could accomplish were we not limited to one lifetime! We-"

The cavern shook, knocking them from their feet, and the iratus suddenly quit backing away. The alien quickly scrambled upright, poking at buttons on a device at his wrist in growing panic until Malenkov snorted, twisting a dial on her own wrist device. The insects backed off, agitation redoubling, making McKay shudder. Lip curling in disgust, she then starting wiping her hand on her pants as Matt let slip a low, hollow bark of laughter. Her hand had landed in iratus excrement when she'd fallen. The alien, meanwhile, had slipped an odd, flesh-colored glove onto one hand, approaching a darkened console near the wall. It lit up at the touch of the gloved hand.

"Honnnored doctor, I must go." The creature's speech contained an odd slur. "They attack again."

She snorted dismissively.

"Go. Tell the council I must have quiet to work! Incompetents."

Her growl was punctuated by another explosion that sent sparks from several machines and the bowing exit of her alien underling. It was then that Matt saw the opportunity he needed.

Tbc…. Yes, really, soon. I promise. This hasn't been abandoned, just on a really long break.


	15. Ch 14: A Time to Kill

Disclaimer: Stargate Atlantis and all characters therein are the property of MGM. This story is for entertainment only and the author is in no way profiting from it, nor exercising any claims to Stargate Atlantis.

Warning: Violence and Swearing

Chapter 14: A Time to Kill

One moment Rodney was glaring at Malenkov, unable to believe the arrogance of the woman, helpless to stop her, and the next she was yanked around, an arm snaking around her neck as she was forced to stand with her back to the cell.

"What the-"

The startled astrophysicist yelped, then noted the hole left in the force shield between two of the bars and sparks flying from the nearby control panel. The explosions must have done some damage! Matt Sheppard had obviously seen the opportunity first, striking as fast as an iratus bug. The elder Sheppard leaned over, mouth just behind the captive women's ear, and Rodney strained to hear the low whisper.

"What's the locking code? NOW!"

Yet another thing Matt had in common with John, Rodney noted absently to himself. Both men yelled and blustered, but when the voice dropped to barely more than a whisper, taking on the edge you knew could cut steel, bad things were about to happen. Malenkov had obviously never taken enough notice of their military commander to work this out. She started to sneer, only to have it choked off by a tightening arm.

"Codes, or you die right here."

"You would let me live?"

Well, at least the woman knew enough to recognize danger when she heard it. Not that Rodney would mind all that much if she refused and gave Sheppard an excuse to choke her. He couldn't stop the bitter retort.

"And why would we want to do that? You tortured him! You're as bad as Kolya!"

Matt shot him a dirty look, but right now he could care less. The woman deserved nothing more than to be dropped on an iratus planet with no gate. Apparently, though, the older man had another plan in mind for their sudden captor turned captive.

"I'll think about it if you tell me how to work the controller on your wrist and directions out of here."

The woman actually had the gall to hesitate.

"Fine!"

The Russian finally spat out.

"You won't live once the Kal'Kor start hunting you anyway! Take a right, then the third left. You might reach the surface in one piece. The button on the top of my device activates the sonic to repel the iratus. The side dial controls the range. Hit π to the sixth digit on the keypad, McKay. If you're actually intelligent enough to know it. Get out! I doubt your precious colonel will live to see Atlantis anyway, even if you do!"

McKay didn't waste breath responding to that one, just reached through the gap, twisting and wincing at the contortions necessary to hit the numbers on the pad. He'd be feeling that for a week, no doubt. The field shut down with a blue flash, the door to their right sliding about halfway open, then stopping dead with a shower of sparks.

The Atlantis scientist turned back in time to see Matt release his grip on Malenkov. The woman stood for a few seconds where she was, either in momentary relief or confusion at the sudden return of unrestricted breathing. It was one second too long. Without hesitation, Matt grabbed her head in his hands and twisted sharply.

_*Snap*_

The sound of bones cracking sent a shiver up and down Rodney's spine as the body fell limply to the floor, sightless eyes now staring into his. He could feel his mouth drop open as he stumbled back a few steps in horror. At first, the ground shaking seemed to be in his head, then the sound of another explosion. For once, he wasn't complaining about having nothing left in his stomach as it heaved in response.

"You- You- She- What- She's-"

"Dead."

The man stepped nimbly around the cell walls, bending to pull the device from the corpse's wrist. There was no emotion in the man's face, no remorse for the life he'd just taken, and for a moment, Rodney couldn't help remembering another remorseless face staring at them through a grainy transmission. His revulsion was cut short as a hand grabbed him by the back of the jacket, yanking him along in the wake of the older man as Matt headed grimly toward John.

"I said I'd think about letting her live, and I did. She'd have had the aliens breathing down our necks the second we left. Now. Move, McKay!"

The sight of the iratus scurrying away from John in response to their approach finally yanked his mind firmly away from what had just happened. His team leader and friend was injured, that had to be his priority now, he reminded himself. He could freak out later. Rodney wasted no time in searching the chair for any way to release the bonds holding the other man even as Matt reached for the blindfold, pulling it from John's eyes. The younger Sheppard immediately began to thrash, fighting the touch with a strength he shouldn't have had left, mouthing words he had no voice to yell defiantly. The astrophysicist stepped quickly back, unwilling to risk cracking heads with his friend, and received his first good look at John's entire face, no longer masked by the cloth.

"Oh, god, that is so not good! What'd they do to him?! Sheppard! Quit thrashing, it's me! McKay! We're trying to get you out of here!"

It was probably futile, but he had to try even as fear rolled through him. The upper part of John's face, all around his eyes, was covered in some type of burn. The hazel eyes themselves rolled frantically around, obviously unable to focus, whites bloodshot. If John even heard him, there was no reaction other then the continuation of the ever weakening struggles. Next to him, Matt's lips had thinned, eyes cold.

"Grab something sturdy and watch the door, McKay. If anyone comes, knock them out."

"But what about-"

An impatient shove cut off the rest of his sentence as the man turned back to his son. Rodney quickly concluded that the better part of valor would be in not further irritating a man who'd just snapped someone's neck right in front of him. A fast glance around for a suitably heavy object yielded the Atlantis computer tablet, much as it pained him to think of damaging the delicate instrument on some thick-skulled neadrethal.

Scurrying to a place just inside and to the side of the doorway, he heard Matt sternly ordering John to look at him. Like that would do any good! Idiot. Rodney risked a peek backwards in time to see the restraints snap open, Matt deftly hauling the all but unconscious man up and out of the chair. Beyond them, the iratus renewed their agitated hiss with renewed strength, pressing as close to the two men as they could force themselves. Another explosion mercifully over road the spine tingling sound momentarily, forcing Rodney to clutch the wall in an attempt to stay on his feet. Whoever was attacking was obviously moving closer. A crash to one side signaled the danger of staying here much longer as a large chunk of rock fell from the ceiling, smashing down into the center of their former cell.

"Shit! Let's get outta here!"

He didn't bother to hide his panic, ducking a bit as he carefully slung an arm around the colonel, taking some of his weight. Blood from John's reopened stitches immediately soaked into his jacket. They needed to get someplace safe, get that stopped.

"Did she say left or right?"

They shuffled along the so-far deserted hallway, stopping momentarily as they came to the cross passage, smoke filling the air straight ahead of them.

"Right! Then third left!"

Matt snapped the directions out without stopping, forcing the other man to scramble to keep up or risk sending them all tumbling. John was barely trying to shuffle now, mostly a dead weight between them, a fact Rodney tried not to think about. If the man could survive a Wraith feeding on him multiple times, then he'd better damn well survive this, or Rodney'd kill him himself!

The eerie silence stretched, broken only occasionally by a distant explosion or yelling, until the scientist became aware of a soft murmur from the elder Sheppard. At first, he thought the man was simply cussing, or something, then he began to pick up on the almost gentle litany.

"Stay with me, John. McKay and I are getting you out. Keep walking… I know you can do this. Just a bit longer…"

It was the last thing he expected from this harsh stranger, this grizzled soldier with the cold eyes. He'd have thought threats and orders more Colonel Matt Sheppard's style, not this almost familiar coaxing. No, this was what he vaguely remembered hearing from his team leader as the man hauled him to the gate after he'd been shot in the… back with an arrow. It'd been a voice he latched onto, a reassurance that his friend would be there, taking care of him, an anchor through the pain. A gentleness few besides his team ever saw, and then not very often.

Then they turned a corner to find themselves face to face with two red-eyed aliens. Rodney staggered as he was almost instantly left to support John's full weight, a next to impossible task with the grip he had. A weapon went off, one bolt zooming past him, but all he had time to do was pray they didn't hit him as he tried to pull the injured colonel back around the corner with him. John, however, abruptly tried to pull away, alerted by the sound or some sense of danger even though McKay could have sworn the other man was all but unconscious a second ago. The brief tug of war sent them both to the ground in a tangle of limbs just as the firing stopped.

"Dammit, Sheppard! Hold still so I can see who's trying to kill us!"

The other man did stop, though probably from weakness, not coherence. Rodney managed to twist around, looking toward the position of the aliens. Only they were on the floor and there were five now, not two. Matt Sheppard stood over them, an alien weapon in each hand, already bending to retrieve another of the iratus repelling devices. Seeing McKay watching him with wide eyes, the man grimaced.

"So much for my retirement!"

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John could feel the pain throbbing through his body, welcomed it as proof he was still alive. Odd that it was his head and arm that hurt the worst, though, not the feeding wound that he remembered on his chest. He squirmed a bit, careful to keep his movements small, trying to discover if he was still restrained without alerting the Genii he was conscious. Something still covered his eyes, making it impossible to open them even if he wanted to, though his arms and legs were free. If he wanted to escape, he needed to see. Cautiously, he reached for his face only to have a hand gently press his arm back down. A weary, wonderfully familiar voice came from beside him.

"Don't Sheppard. Your eyes might be damaged, they need to stay covered until we can get you back to Atlantis."

Rodney, with just enough underlying panic in his tone to tell John that wherever they were, it wasn't completely safe. Which didn't exactly make sense. With a sinking dread, he tried to speak to his friend.

"Rodney? Did Kolya capture you, too?"

Throat suddenly on fire with pain, he desperately attempted to raise moisture in his mouth, swallow to sooth it, even as he registered the fact that no sound had emerged. The hand returned to his arm, tightening in warning.

"Stop that, your throat's raw meat. Let me do the talking." There was a pause, but John wasn't about to try again. "Do you remember where you are?"

He settled for a head shake in answer. Better to get too much information in return than keep guessing. As he lay waiting for a response, though, he pummeled a reluctant mind for further memories. McKay hadn't been in Kolya's compound, he was certain of that. He'd heard the panic in his friend's voice over the com line to Atlantis. Wait… He'd gotten away with that Wraith. Hadn't he? They'd gotten lost in the forest, the Genii came, then- His friends. He'd gone home, as young and healthy as when the whole mess started. A quiet grumble came from next to him, jolting his mind back to whatever situation they'd landed in this time.

"Oh, great. Just don't try hitting me again, okay? I'm not Kolya, or the Wraith, or an iratus bug or whatever else your mind keeps throwing up. We've escaped the bad guys and we're trying to reach the Stargate, but the stupid things on the other side of the planet."

Now the man was plain grousing. Good, that meant he wasn't hurt. He nodded, trying once more to swallow. There was a rustle beside him, then his head was gently lifted, a curved metal rim pressed to it as liquid hit his lips.

"Try a few sips, it's just water."

That he could do, even if swallowing was proving impossible. The water soaked into the dry tissues of his mouth and he savored the relief it brought. A bit trickled down his raw throat, then the container was pulled away, his head carefully lowered back down. He could hear Rodney shifting around then-

_*snap*_

John flinched, unable to control the gasp of fear as the memory of a muzzle flashing in his face filled his mind. Hands. Hands grabbing his shoulders, restraining.

"Sheppard! John! It's okay! It was just a twig I stepped on!"

It was his friend's use of his given name that grounded him, the first time he ever remembered Rodney using it. He relaxed, riding out the wash of pain movement had brought, then mouthed his question, not attempting to put any voice behind it.

"Where?"

He had to repeat it twice more before there was a reply.

"What? Where? Oh! You want to know where we are? If I knew that we wouldn't be sitting here. Listen, just get some rest, because when-"

"A little louder, McKay, I don't think the beings chasing us heard you yet."

The cold, sarcastic voice was straight out of his hallucinations. John stiffened, body automatically attempting to prepare for a flight or fight response though he was too weak to possibly attempt either one.

"He actually lucid or still hallucinating?"

There was a snort from beside him, but he noted Rodney was careful to keep his volume down when he replied.

"He was responding to me. Swallowed a bit of water, too. How close are they? Do we need to move?"

John tried mouthing 'who' but neither man must have been paying attention. His mind raced, racking his still foggy memory for how his father could possibly be here. He'd been certain that was a hallucination! The older man cut through his thoughts, addressing Rodney.

"Not anymore. Here. Put that on John. I don't like how many of those damn bugs are around here."

His good arm was lifted, a band placed around it just above his wrist, but his attention had latched onto the word 'bugs' with a surge of panic. He hated those things! As silence momentarily fell between his companions, he could hear them. Chittering, agitated buzzing all around, surrounding them, filling his ears until his mind blanked once more, enveloped in the suddenly welcome release of unconsciousness.

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Rodney sighed with mingled relief and worry as he heard his friend's rapid breathing slow, body was once more limp in unconsciousness. He knew John was in bad shape, but couldn't deny the spark of hope at finally receiving a response from the man. Maybe, just maybe, their insane luck would hold out long enough to get them home, into the competent (not that he'd ever admit it out loud) care of Carson, because the last two days really didn't bear thinking about.

If the astrophysicist had counted on the nightmare ending when they'd escaped yesterday, he'd been disabused of the notion fast. The ships hovering over the base where they'd been captive weren't anything he recognized or would really qualify as spaceships. They'd looked more like a twisted version of a helicopter, with large rotating arms that moved the blades both vertically and horizontally. Sheppard would've loved them, stupid flyboy.

The beings in them had completely ignored the three stumbling, filthy humans, even when they passed close enough overhead for McKay to see more of the red-eyed aliens operating them. After a lengthy debate, they'd decided to try following the flight path of the craft, assuming, hoping, really, that they came through the 'gate.

It'd taken about six or seven hours after that for the first signs of pursuit to show up. Time enough for Matt to create a makeshift stretcher with the knife he'd taken from the aliens and their jackets to carry John and for them to hike far enough from the enemy base that they barely heard the explosions. They'd taken shelter for the night, then, keeping a wary watch, but none of the groups came close. Another endless, backbreaking day of hiking had followed, until Rodney had insisted on a halt to rest, shoulders screaming from the weight of his end of the stretcher. Matt had promptly handed the startled astrophysicist one of the confiscated weapons and vanished into the thick brush. That had been a little over an hour ago, and the minutes had crawled by, his finger twitching on the trigger at every rustle of the trees around him until Sheppard stirred, distracting him.

Matt had reappeared as silently as he'd vanished, sarcastic comment on his lips as he tossed Rodney another of the alien devices and several canteens of water. The scientist knew better than to ask what had become of the former owner. It had been the longest string of words out of the man since their argument over which way to go early yesterday, Matt Sheppard so taciturn he'd been making Ronon look like a chatterbox. The few times Rodney had dared a question, the only reply he'd received was an icy glare and the military hand sign to keep moving.

When they'd stopped, however, Rodney had heard the whispered litany as Matt tended his son's wounds, bathing his body with most of what little water they had in an attempt to cool the fever raging through the younger man's body. It was a jarring contrast that he couldn't quite comprehend. Stupid, stubborn idiot. With one more weary sigh, the Atlantis scientist heaved his aching body upright, hefting one end of the stretcher and started walking, no rescue in sight.

TBC…


	16. Ch 15: A Time for Hope

Disclaimer: Stargate Atlantis and all characters therein are the property of MGM. This story is for entertainment only and the author is in no way profiting from it, nor exercising any claims to Stargate Atlantis.

Warning: Violence and Swearing

Chapter 15: A Time for Hope

Elizabeth stumbled as she moved into the Atlantis conference room, catching herself on the back of a chair as she met five sets of equally weary eyes. It was just over 60 hours now, and counting, since the Jumper disappeared through the event horizon, two of their own aboard. It felt more like six months. The Atlantis leader eased herself into a chair, gratefully accepting a steaming mug of coffee and reassuring squeeze on the shoulder from Teyla. She met each gaze in turn, her own careful mask finally cracking- Major Lorne, Teyla, Ronon, Radek, Carson. Resolve was firm in the room, shining in the eyes, allowing Elizabeth a boost that the coffee alone couldn't provide. They were all running on caffeine coupled with a determination that this wouldn't end without the safe return of their people, having slept a few hours at most, and that only under the threat of sedation from Carson. However, every hour that went by with no communication with the abductors, no demands, and no new leads, hope dimmed.

"Alright. Updates, please. Major Lorne?"

"We still have a marine missing, the one who was supposed to be guarding the Jumper Bay when all this happened. No sign of him. Teams are still searching the list of worlds Dr. Z was able to pull from the DHD, but so far we're not having any luck with that list either. I'd like permission to start teams on a ground search of all the worlds the list Malenkov is known to have visited."

"I thought you already searched those worlds."

Ronon sat forward, brows drawn in a frown. He'd been having the hardest time of all of them dealing with this, mostly because there was little he could do. Those marines who were off duty were conspicuous in their avoidance of the gym as a result.

"We did, but most are worlds with extensive cave systems that could block the Jumper scans."

"Aye, but she went to worlds with cave systems because that is the preferred nesting area for the iratus bugs, major! You can't send marines in there!"

The angry outburst from the physician met with winces around the table, mostly because they knew he was right.

"Maybe not all of them, Doc. My people would have strict orders to fall back out of any cave the minute they detected signs of the iratus, but even you have to admit a world like that would be a good place to hide."

Lorne glanced at Elizabeth, obviously awaiting her decision, but it wasn't as easy as that, not for her. How would John have assessed the situation? Would he have said it was worth the risk of more lives for the three taken? She dropped her head, idly watching the coffee she swirled in her cup, weighing the debate. 'We don't leave our people behind.' How many times had she heard him say that? And yet, he'd basically ordered her to abandon him to Kolya not that long ago. He must have known how little chance they had of finding him before rescue became recovery! Silence stretched as she could feel the eyes on her. Finally, she locked gazes with Lorne.

"Do it. But they fall back at the very first sign, major. I want that very clear to everyone who searches. John wouldn't thank us for losing more lives looking for him. What about Dr. Chen? Has he been any help at all?"

A disgusted noise from the large Satedan leaning against the wall, but Lorne shrugged.

"He keeps repeating that she never let him in on her main research, to the point that he believes she set up another lab somewhere in Atlantis. He's been helping search teams look for it for about 10 hours now, but…"

"They have to go slowly and check for more iratus bugs. Yes, I know. And the source of those is probably her secret lab. How many have we found so far?"

Teyla took that one.

"So far, ten, including the one in Colonel Sheppard's office, and the one from his quarters. Two were in the Jumper Bay shortly after the colonel, Dr. McKay, and Mr. Sheppard were taken, one was found yesterday morning in the infirmary, one on a balcony, two in the colonel's quarters this morning, and two more an hour ago in the surgical suit."

"Aye. I didn't know that Bethany had such good aim, or that she could swear like that. There is only one thing that all those locations have in common, however. They are all places where the colonel left blood traces behind. I think the things are attracted to him, almost as if he were one of their own again."

Carson quickly held up a hand to forestall the inevitable questions.

"And, no, there was no trace of the iratus DNA in him, not even in the blood left on the floor of the Jumper Bay when he was abducted. The Wraith did leave a trace of enzyme behind that was subtly different from the feeding enzyme. It seemed to act as a stimulant, but with subtle differences from the feeding enzyme that Lieutenant Ford was addicted to, which is why the colonel's health became slightly worse when the bulk of it began leaving his system. What's left now is more akin to the marker left in the blood of those who've hosted Goa'uld. My suggestion is that we concentrate the guards around the areas where we have our people temporarily housed and anywhere the colonel bled, wait for the bloody things to come to us."

"Alright, what about the codes used on the laptop recovered in the Jumper Bay?"

She glanced at Zelenka, keeping her hands firmly around her cup to keep herself from fidgeting. Ronon wasn't the only one feeling like a fifth wheel during this whole mess. There was no one to negotiate with, no one to plead with, and nothing to do but wait and allow her people to do their jobs. Elizabeth Weir had never been all that good at waiting.

"It is a very complex code. We are still working, but… We need Rodney. Or perhaps Colonel Carter. They are the only ones who might do this faster."

At every turn, another roadblock. As she watched, the Czech swallowed nervously, as if he were about to face a jury sure to convict.

"There is something else that I found just before this meeting. The problems with the internal sensors were not a result of the last Wraith attack on Atlantis as we had thought. There was a virus buried deep in our systems, similar to the Trojan virus on Earth, except controlled. If I can find a way to purge it, we should be able to restore full internal sensors for the entire city."

Weir's blood ran cold. Around her, the sound of chairs scraping filled the room as everyone straightened, all leaning toward the engineer in shock.

"A virus."

Her voice dropped, as loud as a gunshot in the stillness.

"The Trust? They did try to blow up the city before, and wouldn't exactly have a reason to be happy with Colonel Sheppard or Dr. McKay."

Lorne's statement met with nods, except from a frowning Carson Beckett.

"There's only one problem with that theory, major. We know that the other being on the Jumper was an alien we've not encountered before. I didn't think the Goa'uld were big on trustin' other species, let alone working with them."

Radek was already shaking his head.

"It shows no signs of alien programming. I agree with the major that the Trust is likely. We should know more-"

An abruptly raised hand cut off the other man as Lorne keyed his radio.

"Go ahead, Lieutenant Paulin."

The major stood even as he listened, then faced Elizabeth.

"Ma'am, Dr. Chen and two of my men think they've found Dr. Malenkov's lab. They've also found my missing lieutenant, Epps. He was locked in there, apparently unconscious. They'd like you, Dr. Beckett, and me down there to take a look at it. Teyla, Ronon, another iratus has been reported in the hallway near Colonel Sheppard's office. The team is requesting back-up."

"Then we will provide it. Ronon."

The two Pegasus Galaxy natives quickly checked weapons and headed out the door, followed closely by Weir, Beckett, and Lorne. The major grabbed her arm at the base of the Control Room stairs.

"Doctor Weir, I'd really prefer it if you carried a weapon. We don't know how many iratus are still around, and I don't exactly trust Dr. Chen. You ordered everyone else required to move around the city right now be armed."

"I know that, major, but there are two marines with Dr. Chen already, and I'm with you. Let's go."

Lorne was left to catch up, grinding his teeth in irritation, while Elizabeth had no doubt they'd both be receiving an earful from her military commander when he heard about it. Provided John was around to do so.

It was a twenty minute walk through the unusually still corridors of the city, even using the transporters, which explained why it hadn't been found earlier. Next to her, Lorne was in full gear with a P90, obviously taking no chances as he yanked her back anytime she strayed ahead of him. Even Carson carried a handgun, nervously twitching at every shadow and overhead ventilation shaft.

There had been surprisingly little grumbling out of the city's inhabitants when Elizabeth had been forced to quarantine all off-duty and nonessential personnel to three easily sealed off areas. Then again, many of them were veterans of that first year on Atlantis, remembering only too well the first encounter with the Pegasus Galaxy wildlife, quick to fill in the blanks for the newer personnel. Add to that the anger at Dr. Malenkov, not a popular person to begin with, and the respect for Atlantis' colonel, and people were willing to put up with whatever was necessary to resolve the situation. It made them feel as if this time, there was something they could contribute to finding the missing men by freeing up military that would otherwise be required to guard the vast inhabited areas. Elizabeth was simply glad not to have another problem on her hands, though she wondered if John truly had any idea what he meant to most of Atlantis.

Finally, they turned a corner in one of the abandon areas to find a dark hallway with an open doorway about halfway down, light spilling out, but no marines. Beside her, Lorne stiffened.

"Stay here a minute, both of you. Doc, make sure you have that gun ready. Something isn't right here."

"Major, shouldn't you call-"

She cut off the whisper in frustration as he walked cautiously away from her, weapon at the ready. Damn the man for being as bad at sparing a worry for his own skin as his CO! Beside her, Carson was fingering the 9 mil. clutched in his hand.

*_Click*_

The distinctive sound of a handgun being cocked came from just behind her seconds after Lorne disappeared into the room.

"Hand me the gun, Dr. Beckett. Both of you keep your hands where I can see them and walk slowly to the room. I'm sorry, I don't have a choice."

The voice was young, scared, and not immediately familiar to her, but she wasn't about to argue. Hands to her head, she saw the gun grabbed from Carson, and then they both began walking. The doorway revealed a small room, two marines on the ground to one side, either dead or unconscious, and Major Lorne in a standoff with Dr. Chen, both fingering the triggers of their P90s. Chen's lips twisted in a cynical smile.

"Now, major, perhaps you would be more reasonable if you wish Weir and Beckett to stay alive. Put the weapons on the floor."

Elizabeth caught the military man's eye, giving a slight nod. The kid behind them might be just scared enough to actually shoot, and she wasn't too certain who his target would be. The P90 and handgun went on the floor, every move slow and carefully nonthreatening. Chen knelt without his aim ever wavering, retrieving the 9 mil before placing his P90 on the counter behind him and covering them only with the handgun. The scientist lashed out with his foot, doubling Lorne over with a blow to the stomach, then grabbed the soldier, pulling the man into a chokehold with the barrel digging into the major's head.

"Much better. Now, you will allow me access to the Stargate, and I will allow the good major to keep his life."

"And why would I want to do that? You helped kidnap two of my people, not to mention a VIP visitor, and let iratus loose through the city! You'll kill him anyway. Besides, more marines will be here in minutes. If you want to leave this room alive, drop your weapons and tell me where Malenkov took Colonel Sheppard and Doctor McKay."

Another sneer, eyes glittering with hate.

"You think me a fool, Doctor Weir? You acted the tough leader when the one under threat was on the other side of a transmission, but what about right in front of you? Do you know what it feels like to have bits of blood and brain tissue spatter your body from the head of a friend? I do. I'll be happy to share the experience with you."

Elizabeth had to work very hard not to gag, mind reassessing the situation furiously. First rule of negotiation, keep them talking.

"Alright, my mistake. We'll walk to the gateroom together, but first you have to tell me why you're doing this. Are you working for the Trust?"

"Epps, get over here and tie the major's hands, then Weir's and Beckett's. This would have gone much smoother had some idiot not let loose the iratus and forced our hand!"

The young man who'd been guarding them came warily around, allowing Elizabeth her first good look at him. It was the lieutenant on his very first tour of duty who'd vanished from the Jumper Bay. So, not a victim after all. The kid's face was white, but grimly determined, a man who found himself with no other choice, no matter how much he hated the course of action he was taking. She'd been right not to push him into possibly shooting. Chen broke into her thoughts.

"Do you actually think I would conspire with those arrogant overgrown pieces of fish bait, Weir? No, the Trust has nothing to do with this. Your precious secrets are not so secret after all, but they will make me very rich. Now, we-"

Lieutenant Epps reached past Lorne and sharply yanked Chen's arm so the gun was no longer against Lorne's head. That one second was all the major needed to plant an elbow into his captor's diaphragm, then grab and break his arm. Almost before Elizabeth could blink, Chen was on the ground, curled in agony around his arm, Lorne standing over him with a gun pointed at the scientist. Young Epps was kneeling a few feet away, hands laced behind his head in a posture of surrender, tears running freely down his face. Horrified light brown eyes met her own, one hand coming around to offer her a piece of paper.

"I- They didn't give me a choice, Dr. Weir. They said they'd kill my family if I didn't look the other way, cover them. They promised no one would be hurt! I c-couldn't- Not the colonel! I-I know the gate address where he is! Please, you have to believe me; I don't know how much longer they'll keep him alive!"

As back-up came pouring into the room along with medical personnel, relieving Lorne from guard duty, she handed him the slip with the gate address.

"Bring them home, major."

"Yes, Ma'am."

TBC… Two more chapters to go.


	17. Ch 16: A Time to Heal

Disclaimer: Stargate: Atlantis and all characters therein are the property of MGM. This story is for entertainment only and the author is in no way profiting from it, nor exercising any claims to Stargate Atlantis.

Title: A Time to Heal

Author: Pyrodragon2006

Chapter 16: A Time to Heal

Soft voices occasionally intruded into the darkness, but with no accompanying sense of danger, threat, or rush of adrenaline signaling the need for forced consciousness. Safe. John drifted, content for now to float in the haze of half-lucidity, not even stirring when he felt hands on him, moving, jostling his head. The hallucinations that he dropped into were disturbing enough, he had no desire to discover if they were real, especially when one voice simply wouldn't go away.

"I don't know, all right?! Sometimes I don't think even Carson knows what he's saying, and he's one of the only physicians I've ever met that I trust."

"Oh, thank you very much!"

A second voice injected, obviously insulted, before the first went on.

"Didn't see you back there. What the hell took you guys so long, anyway? The explosions weren't enough of a clue that there were hidden inhabitants on the planet? It's not like Malenkov had us someplace no one had ever heard of, she's been there half a dozen times in the last two years!"

"Yeah, along with three dozen others, McKay. Plus all the addresses in the DHD of the planet she first took you to, none of which matched."

A third person, weary and a bit disgusted.

He knew those voices, associated with home and safety. Rodney's whiningly aggrieved tone informed him that they were finally away from threats, at least. The physicist had been with him the last time he became conscious, too, when they had been surrounded by _them, _buzzing, legs crawling up him… His mind scrambled back from that, locking the memory away, latching onto the safety of his dreams.

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"Huh."

Rodney McKay stared at the nearby heart monitor as it resettled into the slow beat indicating deep sleep, the same rhythm it had shown for the last 16 hours. With a sigh of disappointment, he turned back to the impromptu gathering in the small infirmary room. Elizabeth Weir, Major Lorne, Teyla, Ronon, Dr. Carson Beckett, Rodney, Matt Sheppard, and Radek Zelenka had all squeezed in, making the room even more claustrophobic than it already was, but this was one time that the mountain had come to Mohammed, as it were.

Both Rodney and Matt were still in scrubs, not having been officially released, though Carson had shown some sense in handling them after he caught them here an hour ago. After a token attempt at returning them to their beds, an agreement had been reached. Matt and Rodney had promised to rest, take their medications, and submit to whatever monitoring Carson thought necessary provided they were allowed to stay in two reclining chairs brought into John's room. Just as well, since the scientist hated to think of what might have occurred had the Scot tried removing either one of them. He'd learned some self-defense techniques during his time on Sheppard's team, and Matt was downright scary. So, the debriefings had now come to them.

"The colonel okay, Doc?"

Lorne turned to the physician who'd bullied his way to his patient's side when the monitor audibly picked up speed, interrupting whatever Rodney had opened his mouth to add.

"Nothing to worry about, major, he's fine. Colonel Sheppard has been fighting the sedation a bit, but he should sleep for a while now. I'm hoping to take the eye patches off tomorrow; the corneal burns are healing nicely. I'll be keeping him on the stronger medications for a few days, though."

"What stronger meds? You've been telling me for the last hour that John wasn't that badly injured!"

Matt's angry accusation cut through the soft conversations like a knife, bringing all eyes to him, wary. No one had decided quite how to handle this suddenly concerned man, a startling change from the harsh indifference bordering on hate from just days before. Carson bristled, eyes narrowing.

"I said none of his physical wounds by themselves were that severe. Combine them, though, while adding blood loss, emotional trauma, exhaustion, and shock, and you have one very sick man. Not to mention the damn drugs they forced down him! I'm keeping him sedated to allow him time to heal without the added stress of what happened. Everything that can be done to make this as easy on him emotionally and physically as possible is being done, I already told you that three times!"

The fierce whisper provoked another string of quickening beeps from the equipment, only subsiding when both Teyla and Rodney placed calming hands on their team leader's arms. Carson, meanwhile, was visibly forcing himself to calm while pinning Matt with an exasperated glare. Rodney had no doubt the Scot now wished he'd followed his friend's helpful suggestion of keeping the older man sedated for a while. He could still hear the cracks of Malenkov's neck snapping ringing in his ears, not to mention haunting his nightmares. And Elizabeth had been unnerved by John during his Genii rampage that first year! Swallowing, he broke the silence with a question he'd secretly dreaded since being rescued late yesterday.

"And mentally? They let those bugs all over him! The first time he woke up after we escaped, he tried to deck me! Even half-dead that man hits hard!"

Winces all around. Well, except for Ronon, who Rodney noted was grinning in delight. He did his best to ignore that. The doctor shrugged in answer, expression tight. Elizabeth closed her eyes momentarily in defeat.

"If we'd found them sooner…"

Lorne was already shaking his head with a frown.

"The mineral content of the rock blocked our scans, Ma'am, or we'd have known there was a civilization down there quite a while ago. Until they escaped, we had no way to know, especially since it was one of the first planets searched, well before the Nal'kor started their assault."

The Canadian's eyes narrowed, mulling over that bit of information.

"The who?"

"The Nal'kor. They were the aliens attacking the compound, McKay. Apparently the ones who had you three are called the Kal'kor; they're a splinter group mostly made up of non-conformist scientists and opportunists who escaped from a Nal'kor penal planet. They've spent the last twenty-seven years or thereabouts hunting them while the Kal'kor ransacked any group who seemed weaker, stealing technology, weapons, food, whatever they could get their hands on. It was sheer luck they cornered them when they did. The Kal'kor had grown sloppy thinking no one would ever look for them on an iratus planet."

"Fairly impressive array of technology for scavengers."

Matt observed sourly, a hand running through his grey hair. Unfortunately, the man had a point this time.

"Yes, about that. How the hell did one of them hide from Atlantis' sensors, not to mention use Ancient technology without the ATA gene?"

The Atlantis leader winced.

"The Nal'kor asked one of their prisoners that. Apparently they discovered a warehouse of sorts where the Ancients were collecting and studying a variety of technologies from races throughout the Pegasus Galaxy. When the war started, it was abandoned and noted as destroyed in the Atlantis database, which is why we never bothered to send a team."

"Well, obviously that was wrong!"

McKay interjected with a roll of the eyes.

"To use the Ancient technology, the Kal'kor found gene carriers among the local populations and… salvaged parts. Anything that didn't require a mental component, such as the cell force fields, could be used if they wore a glove made from the skin."

Carson added, distaste and disgust with the method clear.

"That's why you and Matt were kept alive, Rodney. They were saving you until they needed a part."

Teyla was just quick enough with the nearby emesis basin, since there was no way the scientist could have darted through this mob for a toilet. Lunch certainly tasted a lot nastier coming up, not to mention the pain of already sore abdominal muscles being forced to spasm once again. Ronon was ready with a cup of water for him to rinse his mouth, then the basin was passed to a nurse waiting in the doorway.

"Gah! That's just…wrong on so many levels! How did you find all this out, anyway? There aren't more of those Kally Kon things waiting to escape again, are there? You destroyed their DHD or something, right? Well?!"

Looks all around warned him Matt wasn't the only one some wanted to sedate. Lorne rolled his eyes, but answered patiently enough.

"We learned this from the Nal'kor, Doctor McKay, who were also kind enough to allow us to salvage any equipment we could, Ancient or otherwise, as an apology of sorts. It's all waiting for you in your lab. As for the Kal'kor, the Nal'kor had their own solution to that threat. Said they couldn't take the chance of leaving any alive to create more trouble, especially now that the Wraith are awake again and could notice a relatively advanced alien race around. They killed them all. By the way, I saw Malenkov's body. It looked as though her neck had been broken."

Even before the military man glanced at him for an explanation, Rodney was vigorously shaking his head. He wanted no part of that one!

"Don't look at me, ask the king of bi-polarism over there. He did it."

That earned an icy green glare.

"I did what was necessary, McKay. Can any of you tell me who was behind all this in the first place? Malenkov implied she had backing from Earth, which she further insisted wasn't the Trust."

"Dr. Chen told us the same thing, but refused identify them. Fortunately, Lieutenant Epps was more forthcoming, especially after we contacted the SGC yesterday and they assured him that his family would be protected."

Rodney cocked an eyebrow at Elizabeth's explanation, but Matt beat him to the question.

"How does he fit into all this?"

She settled back into her chair, silent for a moment, then shrugged.

"Apparently the lieutenant has cousins in Los Angeles who tangled recently with the Russian mob. They're the ones behind all this. Malenkov had ties to them stretching back to the Communist years that she'd buried, so when she was assigned to the Stargate program, she funneled the mob information and they backed her work. When Epps' family came to their attention, they found out about our Lieutenant being newly assigned to Atlantis, not to mention young enough to intimidate easily, and took advantage of the situation. They used a mole the SGC is working to find right now to place photographs and personal items from his uncle's house in his quarters at the SGC along with threats. Epps didn't know who to trust, and the requests appeared to be fairly innocuous, such as allowing Malenkov off on her own off-world, so he went along with it. When they started threatening Colonel Sheppard, however, he decided he had to do something. Epps is the person who released the iratus bugs, hoping it would alert us to Malenkov, and when that didn't work, he went after her in the Jumper Bay, which is probably what John walked in on. Chen knocked both John and Epps out, then Rodney and Matt, but kept Epps in Malenkov's second lab, which is where we encountered him yesterday. He helped us subdue Chen and gave us the address of the planet where you were."

"What will be done with him now?"

Teyla softly asked Major Lorne, one hand still gently stroking John's arm where she stood on the far side of the bed with Carson.

"Right now he's confined to quarters. General Landry said he wanted the full reports on the incident as well as Colonel Sheppard's recommendation before determining what to do. It's pretty tricky court-martialling someone when most of the information is highly classified. My guess is that they will return him to Earth and either give him a quiet discharge or a duty station where he can't be of any use to anyone, like McMurdo. Either one would be getting off lucky after what he did, duress or not."

The military second-in-command left no doubt as to what he thought of the young man, though the astrophysicist was finding it strangely hard to be angry with the kid. Blame him, definitely, especially considering the fact that he'd let those damn bugs loose in the city. It still had him looking over his shoulder even though he'd been assured by Carson that all the things had been dealt with. Then again, he also distinctly remembered the horror on his friend's face when John had awoken to one sitting on him. Okay, maybe he could be ticked. Rodney cringed at his own mental bad pun. Best not to try that one on Sheppard for a while, though.

-------------------------------------------------------------------------------------------------------------------------------

John fully regained consciousness to the unpleasant sensation of liquid dripping into his right eye as the lid was forcibly held open. He jerked away, trying to fend off the source only to feel hands once again restraining him. Abruptly, the lid was released, allowing his eyes to snap closed. A voice caught his attention before he could descend back into the nightmares.

"Colonel! It's alright, you're safe! I didn't intend to wake you like that. I'd already put the drops in your other eye and you didn't stir."

The Scottish brogue was unmistakable and he relaxed into the infirmary bed. Home.

"Rodney?"

The rough croak that emerged bore no resemblance to anything remotely human, let alone understandable, serving only to re-ignite the extreme burning in his throat.

"Don't try to talk, John. Dr. Beckett says it may take a few more days for your throat to heal. It's still pretty raw. Try opening your eyes now that I've turned the lights down."

John's breath caught at the voice, trying to decide how to respond. It was his father, except his voice was filled with the gruff gentleness he'd usually only shown around Mom or Melissa. Where was his team? They were never far away until the ill or injured team mate was well on the road to recovery. One way to find out was to _look_, he told himself sternly. His eyes watered from the light, even if it was dimmer than previously. Someone carefully blotted the tears away before they could sting the burns on his face. An ice chip was slipped into his mouth, the cold wonderfully numbing as it slid down his raw throat. Slowly, the faces of the two men swam into focus, both watching him intently.

"You have a corneal flash burn and minor surrounding burns to the tissue on your face, colonel. "

Yeah, he definitely knew that, recognized the symptoms from when he'd suffered one in Antarctica when he was first stationed there. Course, that one had been his own stupid fault when he'd forgotten his sunglasses while flying over snow, the glare causing the burns. It was one reason that he ensured he always carried his aviators on missions when no one else seemed to mind the sun. John rolled his head to glance pointedly around the familiar back room of the infirmary. A soft chuckle let him know that words weren't always necessary to communicate, Carson understood him perfectly.

"I sent them to drag Rodney to the mess hall, make sure that he ate. All three of them should be back soon. They haven't left your side except when I forced them out for the last three days, Colonel. Now, I need you to answer some questions for me. Just shake your head yes or no."

That he could do.

"Do you know where you are?"

Ah, start with the obvious. He nodded. Atlantis, home, safety, a second chance, the weight of responsibility he'd never sought but found himself within. That's where he was.

"Do you know who I am?"

He certainly hoped so; they'd been spending way too much time together lately. A nod and wry, slightly guilty smile received an amused snort from Carson.

"Good. Do you remember your father coming here to Atlantis?"

How could he forget? John looked away, blinking rapidly against the rush of emotions that brought to the fore with the memories, especially of their last encounter on the balcony. The very idea that he would have turned his back on his mother and Mel like that still stung.

"And what happened after?"

Now that was cheating. He carefully extracted a hand from his father's grip, waggling it. The jumbled mess in his mind wasn't all that helpful, almost nightmarish since he wasn't positive what was memory and what was hallucinations, nor was he that eager to find out. He heard the heart monitor pick up, betraying his unease.

"Its okay, John, you're safe, just relax. That's it."

"Don't tell me I finally leave and he's actually awake!"

Rodney's disgusted voice rang out, making John jump slightly while Carson shook his head and his father rolled his eyes in exasperation. Rodney, Teyla, and Ronon entered, smiles widening as John struggled to force his weary, aching body into sitting up. The bed rose up beneath him, allowing him to settle into its support. Both of Rodney's hands were wrapped in a light layer of gauze, causing John's eyebrows to rise in frustration at being forced to silence. What had happened? He glanced around, but not spotting what he wanted, he made a writing gesture. His father picked up on it first, fishing his ever present small notebook and pen out of his pocket and handed them to his son. For one of the first times he could remember, John was grateful his old man was such a creature of habit.

"Okay?"

He wrote, fumbling to keep the notebook propped on a raised knee to avoid jarring his injured arm. Matt took it, reading the question aloud, and then turned to his son, reassurance on his face.

"Doctor Beckett says you'll be fine, John. You just need-"

"Oh please! "

Rodney interrupted with an eye roll.

"That's not what he's asking. I'm fine, just some blisters and a few splinters. Carson has me on Tylenol. Ronon and Teyla weren't even shot at, let alone injured. Everybody's fine except you!"

"Aye, and you yelling isn't doin' any good, Rodney. Now, the colonel needs quiet and rest to recover. You've seen him, now get out, all of you. I'll let you back in to see him tomorrow. And before you ask-"A finger pointed at John's nose, "You're still running a mild fever and recovering from multiple injuries, so you won't be released to your quarters for at least several days."

John couldn't help the catch in his breathing at the mention of his quarters, memory pulling up waking up with an iratus bug on his chest. No, he definitely wasn't up to facing his room just now. The Doc was watching him, narrow-eyed, and the officer realized he must have missed something. Crap, now he'd never get rid of Heightmeyer. Teyla stepped forward then, laying a calming hand on his arm.

"I hope that you will not be angry with us, John, but we re-arranged your room. Ronon told us that you had been considering changes, and Kate assured us that it would be beneficial. Your office has also been moved to a more convenient location near the Control Room and teams' Ready Room."

He was too exhausted to be anything but grateful to them at this point. They were his family, the people he trusted the most. John simply squeezed her hand, knowing the perceptive woman would pick up on the emotions in his eyes. A clearing throat brought his attention back to his father.

"Actually, I have something to say to John, but I believe I owe it to all of you, as his team, as well."

The older man took a deep breath, clearly nerving himself up to voicing his thoughts.

"I'm sorry, John. I was wrong. For what I thought and did four years ago and for the way I've acted since coming here. I don't know if you can ever forgive me, but… You've done one hell of a job here, Lieutenant Colonel. You should be proud, and don't ever let anyone, least of all me, tell you otherwise."

Shock washed through him, leaving him gaping. If he'd had a voice right now, that would've stolen it. Matthew Sheppard didn't apologize, certainly not to his son! Had he ever heard the man admit he was wrong when not confronted with a superior telling him so? How did he respond to that? Thankfully, Matt didn't seem to expect one, pushing himself to his feet, but paused in the doorway, meeting John's conflicted gaze. Then he met the eyes of each John's team next, nodding soberly to each.

"I hope all of you will accept my apology as well. I have a friend, John's godfather, who keeps telling me I won't let myself see things that are right in front of my face until I get hit over the head with them. Guess he was right this time, damn him. Not that I have any intention of telling the smug bastard that, commander-in-chief or not. Good day."

With that, he left, leaving five stunned people in his wake. John couldn't help bringing to mind his mother's favorite Bible verse, her voice still whispering it late at night after he'd exhausted himself crying, the aftermath of a fight with his father.

"_To every thing there is a season, and a time to every purpose under the heaven: A time to be born, and a time to die; a time to plant, and a time to pluck up that which is planted; A time to kill, and a time to heal; a time to break down, and a time to build up; A time to weep, and a time to laugh; a time to mourn, and a time to dance; A time to cast away stones, and a time to gather stones; a time to embrace, and a time to refrain from embracing; A time to get, and a time to lose; a time to keep, and a time to cast away; A time to rend, and a time to sew; a time to keep silence, and a time to speak; A time to love, and a time to hate; a time of war, and a time of peace, John." _(Ecclesiastes 3: 1-7)

It was the only verse that John had actually memorized, mostly because of her. Perhaps now, both he and his father would find it was time to heal.

It was Rodney, who'd looked awfully pleased with himself through the elder Sheppard's speech, who caught it first, jaw dropping open.

"Wait a minute! Did he just call the President of the United States a bastard? And your godfather?!"

**Please READ!!!!**

**A/N: The next chapter is the Epilogue, which takes place after the end of the series, which is why this chapter was written as an end to the story for those of you who haven't seen Season 5 as yet. Thank you again for all your reviews, hanging in there with me for almost three years!!! Please, let me know if you would be interested in more stories exploring the restoration of Matt and John's relationship as the series progressed. I have some ideas, but am not sure if they are worth pursuing. Kerri**


	18. Epilogue: A Time to Celebrate!

Disclaimer: Stargate: Atlantis and all characters therein are the property of MGM. This story is for entertainment only and the author is in no way profiting from it, nor exercising any claims to Stargate Atlantis.

Title: A Time to Heal

Author: Pyrodragon2006

**Warning: This takes places after the series finale! Spoilers!**

Epilogue: A Time to Celebrate

_Two and a half years later—_

John smiled as he set down the framed photo of his mother and sister, straightening his dress blues. He still missed them, but it was an ache no longer surrounded by the bitter taste of anger and betrayal. Time really did help heal, even if there were newer, fresher, wounds added along with the photos of Elizabeth, Carson, Kate and Jinto to his memorial shelf. Only two weeks ago, they'd come so close, too damn close, to adding another. Ironic, that he had the Wraith to thank for Ronon still being with them instead of another face captured in time in a gilt frame. The 'what ifs' still haunted his nightmares.

A glance at his watch told the officer he'd better get moving or risk being late to greet the latest set of VIPs, a task that had him wishing for a mission into a Wraith stronghold instead. With Woolsey closeted by the IOA, however, still answering their unending questions and concerns, the tour guide duties devolved to the city's military commander and second-in-command, an unavoidable evil. And he wasn't even allowed to shoot any of them anymore, though that senator really had it coming when he asked for a demonstration of a Wraith stunner. Marines were paid to be targets for the bad guys, not some curious beaurocrat.

If this kept up at the current rate of at least one tour a day, John decided as he set a brisk pace down a strangely empty hallway, he might have to resort to allowing Ronon to scaring a few visits short. With the city in a shambles after their desperate jump to Earth, fight with the Wraith super-Hive, and rather hard landing, there simply weren't enough hours in the day. In addition to the stupid tours, the colonel had his own debriefings, endless reports Woolsey would normally take care of, repairs to oversee and aid with when necessary from the Control Chair, and all of his normal duties as military commander. Granted, that last had slacked off quite a bit with their location and lack of an active Stargate, but still, the only ones busier were Rodney and Radek. John laughed softly to himself. At least his friend had stopped complaining about the force of the _last _landing Atlantis had made, swearing never again to allow Earth to pull away their pilot when about to move the place.

Fortunately for all three men, Teyla and Ronon had taken it upon themselves to bring meals, sit upon their friends when necessary to make sure they actually ate, and enforce at least a few hours of sleep a night or they'd have long ago collapsed. The two Pegasus natives understood too well what was driving the exhausting pace. All of them wanted the city home where it belonged in Pegasus, the unfinished work there hanging in the back of everyone's mind, taunting John with the thought of allies unprotected and the Wraith culling unchecked once more. At least with three ZPMs, returning wouldn't be a problem, albeit a bit slower than the trip to Earth since there was no need to use the riskier, faster, option.

"Sheppard! About time you got here!"

The good-natured hail jolted John from his thoughts to note the Puddle Jumper already at rest on the East Pier. Not the usual landing stop, but the IOA felt it was more impressive than the drab Jumper Bay for their guests' first look at the fabled city. The colonel had grudgingly agreed when he greeted the first batch last week, Atlantis' Control Tower rising behind him and the Golden Gate Bridge in front. Major General Jack O'Neill didn't seem to be taking note of the scenery, however. John straightened hastily into attention in front of the senior officer.

"Forgive me, sir, I was told 1400."

Crap! Being given the wrong meeting time for a Jumper bearing the head of Homeworld Security and the newly named Secretary of Defense was _not _the way he needed his day going! He'd already spent the last six hours in the Control Chair_, _a dull throb picking up beat behind his eyes. If this kept up, he'd have no choice but to slip away at some point to cajole some ibuprofen out of Dr. Keller. O'Neill, meanwhile, glared at him for a moment, kicking up John's headache another notch before snorting and rolling his eyes.

"Oh, relax. I'm not in the habit of firing people for my own mistakes! I missed a time zone when I calculated arrival time."

There was a low laugh from inside the Jumper and a second man moved into the sun, joining them.

"Considering it was Jack O'Neill in the drivers' seat, I'm just glad to get here in one piece without getting shot at!"

John smiled, holding out a hand in greeting as O'Neill nailed the other man with a wounded expression.

"Mr. Secretary, congratulations on your appointment and welcome back to Atlantis."

"Thank you, Lieutenant Colonel Sheppard; it's good to be back."

Amusement at the stiff formality of the greeting sparked in the SecDef's green eyes while next to them, the general rolled his and groaned, sounding more like a bored kid than a flag officer.

"You two are killing me here!"

Matt Sheppard grinned at Jack O'Neill's complaint, and then raised an eyebrow sternly at his son.

"I trust you left the giant ticks and insane scientists behind in Pegasus? Or should I be worried about taking another unscheduled swim?"

John's own lopsided smile appeared as he relaxed into his version of a parade rest.

"Nope, I'm afraid it's been fairly boring around here lately unless you're a member of the repair crews. Sorry. The reception is scheduled for 1430 in the gate room, as you requested, General. I'm afraid I haven't seen the decorating, I've been in the Control Chair since 0800, but Major Lorne assures me everything is per your specifications."

"Excellent."

The colonel gestured the two older men into the cooler interior of the city, deciding against taking the transporters. They had plenty of time for a walk as he'd been fifteen minutes early to meet them anyway, plus there were several points of interest along the way. Besides, he was enjoying his father's company, a slow but welcome change from their previous relationship, or more precisely, their lack of one.

Oh, there'd been bumps aplenty along that road- misunderstandings, shouting matches, and the simple miscommunication that came with trying to heal a relationship from two separate galaxies, but they'd both kept at it, finally putting that Sheppard stubbornness to good use according to John's team. It'd been a pleasure for the young colonel, once he was convinced his father was sincere, to show off his base and all they'd accomplished in the Pegasus Galaxy. It'd also given John a positive focus outside of his recent traumas, a break that both Carson and Kate had happily gone along with in those three weeks before his father returned to Earth to advise the President.

After the older man left, John had established e-mail contact, finding another unexpected benefit of the renewed relationship. There'd been no need to worry about clearance levels or leaks with his father, just a steady presence on the other end of those e-mails, someone who understood not only the weight of command, but also the unique circumstances that often defied the conventional rules. Matt had been happy for any role in his son's life, and so proud to be trusted as a sounding board that he was careful never to judge his son, giving in before the arguments grew too heated. Instead, he treated John as a fellow officer seeking private advice, and asked his own questions in return, still not all that comfortable in his own role as presidential advisor. That connection had kept John steady on those dark days after the loss of first Carson, then Elizabeth, and gave him the strength to keep going when Teyla was taken by Michael. It had also brought out a renewed confidence in John, giving him the comfort level he needed to grow in his command while dispelling some of the isolation and loneliness of high position that not even his team could completely dispel. It was this, more than anything else, that had brought forgiveness and true healing at last.

This had led them here, over two years later, walking the corridors of the legendary city that had at last returned to its birth place. After several minutes of silence as they passed by two work crews, Matt gestured at some of the obvious damage.

"So, how is everything going with Atlantis, John? The Senate had me busy with confirmation hearings, so I haven't been able to keep up with your reports."

"We took quite a bit of damage but nothing that can't be fixed eventually. Colonel Carter arrived this morning, which has helped a lot, even if most of the city had to change their com frequency to avoid the arguments."

John gave what he hoped came off as a tolerably amused smile, fighting against a renewed wave of exhaustion. The chair had taken more out of him than he cared to admit, especially on top of being chronically short of sleep lately. How many hours without work had he managed in the last two days? Four? And that was only in chunks of up to an hour before another call came in. Turned out O'Neill wasn't the only bigwig bad with time zones, he'd had some insist on dropping in at midnight last night. Or was that the day before?

A sharp glance from his father told him he wasn't hiding the fatigue as well as he'd hoped. Damn! The last thing he needed was to give the impression he didn't have time for the reception honoring a Cabinet level Secretary. Especially when said secretary was his occasionally rank-touchy father! Besides, if he kept this up, one or both of the men with him were likely to sic Beckett _and _Keller on him!

"And how have Teyla and Ronon found Earth? Taken them to see the sights yet? I know that Ronon didn't see much when you were here last year for your grandparents' funeral."

John struggled to maintain a neutral look, mind racing to figure out where the hell his father was going with this. Was he baiting him? Sure, he'd had to leave his mother's parents' wake shortly after arriving, but his father knew damn well it was because of a Replicator loose on Earth! The job came first; Matt had drilled that relentlessly into his head as a child.

"Ah, no, not yet. "

How to phrase this so that it didn't sound like a complaint to O'Neill?

"The repairs and everything plus visitors have kept us all fairly busy. Teyla has Torrin and Kanaan with her, too, and Ronon's been helping break in some new international military members the SGC sent over."

O'Neill let loose a low, wicked chuckle.

"Emphasis on 'break' from what Teal'c tells me. "

Matt laughed, smirking in agreement, and John relaxed, glad he'd successfully dodged that one only to have the general stop him with a hand on his arm.

"Colonel, after this whole shindig is over, you're taking the next two weeks off."

The colonel's gut clenched as a thousand and one reasons that couldn't happen floated through his head. Next to him, his father was giving a satisfied nod. Shit! So that's what the whole thing was about! He wanted John to take a break without seeming to play favorites by manipulating, or possibly conspiring with, O'Neill to order it! Very sneaky.

"Sir, with all due respect, I can't leave the city while the IOA has Woolsey-"

A distinct feminine voice cut him off as Colonel Samantha Carter joined them from a side corridor, also dressed in her Class A uniform.

"That's one of the reasons that the launch of the _General Hammond_ was delayed for a month, John. I'm not just here to help with repairs. Cam Mitchell will be joining me tomorrow, too. I think between the two of us, we can keep your city in one piece for a few weeks without you."

"Besides," Jack O'Neill smiled smugly at him, "I'm not in the habit of making requests, Colonel. That was an order. You try setting foot in this city before the two weeks are up for anything short of a Wraith invasion, and I'll… I'll… What'll I do, Carter?"

Sam ducked her head, laughing at her old team leader.

"You'll have Ronon shoot him, then Dr. Keller will sedate him and we'll ship him to northern Minnesota, sir. Not that they aren't both contemplating doing just that already, John, so I suggest you cooperate."

The Atlantis colonel narrowed his eyes at his one-time CO, but didn't say anything. Sam Carter might just carry through on the threat, even though she knew how much he hated being 'handled'.

"I'm fine."

John finally responded evenly as they approached the Gate room, ignoring several skeptical snorts.

"I'm sure Teyla and Ronon wouldn't mind some sightseeing, though. Guess I can't really say no to some time off either. It's been an interesting year. Thank you, Colonel Carter, for coming to oversee the city. I couldn't think of better hands to leave her in."

That sounded gracious enough, considering he'd just been _ordered_ out of his own home! Besides, he could give Amelia Banks leave at the same time. She'd probably love to play guide for Ronon, which left him with Teyla and her little family. He could handle that; maybe finally get her on a Ferris wheel. With a start, John realized he was actually looking forward to this, planning activities to fill his surprise forced vacation. Plus it wouldn't take three weeks on the _Daedalus_ to get home again!

"John…"

Matt's hand on his elbow stopped him just short of the small ramp as Carter and O'Neill moved into the large sunlit room beyond.

"I was ordered not to say anything, but I know how you react to surprises, so… The Pentagon is making some changes to the military side of Atlantis. I'll be announcing them today. You'll still be military commander, with the job you've done; they wouldn't take that away even if O'Neill and Landry weren't on your side, but… Well, you'll see. "

He walked off, leaving the pit of John's stomach dropping into his spit-shined regulation shoes. Just what did that mean? And how come no one had consulted him if they all thought he was doing such a good job? The brass usually at least warned a base commander before they pulled the rug out from underneath him, especially when the SecDef was sent to do the pulling! Face set in stony resolve to hide the broiling emotions underneath, John moved into the nerve center of Atlantis after them.

And paused in shock, turning slowly to survey the transformed space. A lectern with the seal of the Department of Defense stood in front of the silent gate, the flags of the Air Force and Marines behind it. From either side ran the flags of the nations represented in the Expedition along the edges of the platform, with the exception of the Stars and Stripes. Two of _those_ hung from the railings on either side of the central stair case, with two honor guards, one Air Force, one Marine, by them. In the middle was seating on the floor as well as along the Control Room balconies, plus on the staircase itself, and there were still people without a place to stand or sit.

John had planned for most of the American members of the Expedition to show up, plus the senior staff, but this… It looked as though every member of the entire Expedition was here, plus a group from both the SGC and the IOA. Civilians were dressed in suits or dresses, including Woolsey standing with the rest of the senior staff, and the military were all in full formal uniform, a fact that clearly showed the multi-national nature of that contingent, normally easily overlooked unless one paid attention to the flags on the normal Atlantis uniform. The room appeared to be overflowing, a condition John had never seen it in.

As he moved fully into the room, the Atlantis military snapped to attention as one, saluting the city's military commander. Swiftly, he saluted back, as crisply as any drill sergeant- or his father- could want, puzzled by the sudden show of respect from his men and women. That hadn't exactly been in the plan, at least not the one given to him, but he spun, determined to complete his part so that he could claim the more unobtrusive seat in the front row with his team. The lieutenant colonel rigidly saluted O'Neill, Landry (where had he come from?), and his father, then walked over to the open spot between Rodney and Teyla. Beside her, he noted Kanaan, Lorne, Zelenka, Carson, Keller, and Amelia Banks, with Ronon, Carter, Teal'c, and Dr. Daniel Jackson on the other side of Rodney. As he turned smartly in place, the baby in Teyla's arms began squirming to reach out for him, and he willingly took the little boy before he could start to fuss, a move that received a slight amused smile from Matt Sheppard. Looking slightly nervous, General O'Neill approached the microphone.

"Thank you, everyone, for responding to my order- uh, I mean request- to be here today."

A ripple of laughter made its way through the room as John shifted Torrin uneasily. He hadn't heard of any order. Just how much had been happening right under his nose?

"Before I turn this microphone over to our distinguished guest, I want to personally convey my congratulations and thank you to all of you for a job well done. Not to mention for saving our collective asses two weeks ago!"

More laughter came with some scattered applause.

"Now, it is my privilege to be able to introduce to you the newly appointed United States Secretary of Defense, Matthew Sheppard."

Applause, which John sheepishly realized that he couldn't join in on with a squirming one year old in his arms. Matt raised an eyebrow at him as the older man waited out the clapping.

"Thank you, General O'Neill, everyone. Some of you may remember that this is my second visit to your wondrous city, and I must say I prefer this welcome over the last one!"

On either side of the colonel, his team tensed a bit, and uneasy shuffling was heard from behind them. If Matt had been going for a joke with that, it'd gone over like a lead balloon. Not the best start. The Secretary cleared his throat and gamely continued.

"I want to add my congratulations to the general's, along with the assurance that we know that for many of you, the job is not yet done. Soon, this city will return to its ongoing mission in the Pegasus Galaxy. To that end, the IOA has approved expanding the scientific side of the Expedition and requested a similar expansion for the military from my department, a request that the President has granted. In order to do so, however, some changes must be made, which I am here to announce. Along with added personnel, an F302 wing will be stationed on Atlantis, under the command of the city's military commander to be used at his discretion. Any and all military actions taking place in the Pegasus Galaxy will be under his operational command for the duration of the action. For those of you who are civilians, I'll translate that. Atlantis' military commander will be in overall command of all forces, including the _Daedalus_ or any other Earth ship, during military actions. This will prevent a reoccurrence of military action taken by a ship's commander against the advice of the Atlantis commander, an oversight that was directly contributory two years ago to the loss of Dr. Elizabeth Weir."

An angry mutter from the civilians and nodding heads showed that they understood that one, all right. It had been no secret within the city that neither Weir nor Sheppard were exactly pleased with the _  
Apollo'_s preemptive strike on the Asuran homeworld, even if John had acknowledged the necessity. However, it left him in one giant pickle, since all the ship commanders were full bird Colonels, technically outranking him.

"In light of these changes, I have one other announcement. The IOA asked recently for your assessments and advice on the leadership of this Expedition. While the United States military alone determines the identity of Atlantis' military commander, it was agreed to take into consideration your recommendation. To a man and woman, all of you responded with just one name, which happened to match the decision of Generals O'Neill and Landry. You all came here today to honor that uniquely deserving individual as we bestow upon him the rank that is due the military commander of this fabled city, whom I have the honor of calling my son. I would ask that he now step forward, provided someone would relieve him of the youngest Expedition member first."

Solid laughter roared through the space as Teyla quickly took her son from John's arms as he stood there, dazed. It wasn't possible that meant what it sounded like! Was it? A firm hand from the other side of him pushed, starting the reeling man stumbling forward until he abruptly forced himself to pay attention to his walking so he didn't end up on the floor. John was barely aware of his team falling in behind, an unofficial honor guard. Before he had quite wrapped his head around it, the oath was administered, sealed by a kiss on the cheek from Teyla, and his silver oak leaves were replaced by silver eagles by Ronon and Rodney. His team moved to his side once more as Matt Sheppard leaned into the microphone.

"Atlantis, I give you your military commander, _Colonel_ John Matthew Sheppard!"

The approving cheer echoed through the Tower and his ears as John found himself caught in his father's embrace.

**The end. Thank you all so much for reading. **


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